- phenixbb - phenix-online.org

map-to-model FSC on low resolution map
by bluufive2＠gmail.com 25 May '25

25 May '25

Hello, As part of a reviewer request for our manuscript, we are attempting to generate map-to-model FSCs for two low-resolution cryo-EM reconstructions—one at 10 Å and the other at 20 Å. We’re encountering an issue when using mtriage(both standalone and as part of the comprehensive cryo-EM validation pipeline), where the map-to-model FSC values are reported as “None”. For the 10 Å map, we were able to obtain a valid halfman-halfmap AND map-model FSC by supplying the two half-maps rather than the final unfiltered reconstruction. However, this approach has not worked for the 20 Å map, and we are still unable to retrieve a map-to-model FSC. I initially suspected the issue might be related to masking, but it appears that mtriage does not support the use of a user-provided mask. If you have any insight into what might be causing this or suggestions for alternative approaches, we would greatly appreciate your input. thanks best Jesse Hansen

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Excluding atoms from real-space refinement
by elwood.mullins＠vanderbilt.edu 14 May '25

14 May '25

Is it possible to exclude atoms in real-space refinement? Older posts seem to indicate this is, or at least was, only possible in reciprocal-space refinement. Has that changed? Using reference restraints as an alternative is less than optimal. Any help would be greatly appreciated.

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Integrative Structural Biology Summer School Padua Italy 7-11 July 2025
by Roberto Steiner 13 May '25

13 May '25

Dear All We are now at capacity for the Integrative Structural Biology Summer School www.school2025.cristallografia.org<http://www.school2025.cristallografia.org> that will be held in Padua, Italy 7-11 July 2025 However, given the interest we have decided to re-open the registration form as we have been able to secure a slightly larger room for lectures and tutorial. Registration will close this Friday at 5pm CET. With best wishes Roberto (on behalf of the organising committee) Roberto A Steiner www.steinerlab.org<http://www.steinerlab.org> https://twitter.com/steiner_lab roberto.steiner(a)kcl.ac.uk<mailto:[email protected]> Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.steiner(a)unipd.it<mailto:[email protected]> Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours.

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POSITION AVAILABLE: Visiting Research Specialist Position at the University of Illinois at Chicago
by Yury Polikanov 03 May '25

03 May '25

*Visiting Research Specialist Position Available in the Polikanov Lab <https://sites.google.com/view/polikanovlab>Department of Biological Sciences, University of Illinois at Chicago* *The Polikanov Laboratory <https://sites.google.com/view/polikanovlab> in the Department of Biological Sciences at the University of Illinois at Chicago is looking for a talented, skillful, and highly motivated researcher to fill the Visiting Research Scientist position to study the structure and function of the bacterial ribosome.* For full consideration, please submit your application along with a Cover Letter, CV, and three references by May 31, 2025. Cover letter should describe previous research accomplishments and scientific interests as well as how these fit within the scope of the research in the Polikanov lab. Questions can be addressed to Yury Polikanov at yuryp(a)uic.edu. Visiting Research Specialist- UIC Department of Biological Sciences, Polikanov Lab Hiring Department: Biological Sciences Location: Chicago, IL USA Requisition ID: 1033622 Posting Close Date: 05/31/2025 Link to Apply: https://uic.csod.com/ux/ats/careersite/1/home/requisition/14681?c=uic *Position Summary:* The Polikanov Lab is seeking a Visiting Research Specialist. Successful candidate will conduct research by using X-ray crystallography and cryo-EM techniques to obtain a structural basis for various functions of the bacterial ribosome and its inhibition by different small-molecule inhibitors. The successful candidate should have a strong theoretical background in standard biochemical, molecular biology, and biophysical methods, as well as practical skills in the most standard methods currently used in molecular biology and biochemistry (such as protein expression, purification, etc.). Knowledge in X-ray crystallography or other structural techniques is desired but not required. The successful candidate would conduct research and assist with training laboratory personnel in various techniques, experiments, and the appropriate use of research equipment. He/She would also perform data analysis and manage, document, and help with the dissemination of research activities for publication and outreach. *Duties & Responsibilities:* - Record keeping: log and track inventory of chemicals, reagents, and lab supplies - Maintain accurate records of experiments, procedures, and results - Keep the laboratory clean, organized, and free of contaminants - Glassware & Equipment Maintenance - Prepare culture media, buffers, and reagents according to protocols - Assist other researchers in the lab in conducting experiments - Purify bacterial ribosomes and all additional components necessary for the experiments, such as recombinant proteins, tRNAs - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry *Minimum Qualifications :* - Bachelor’s degree in biology, chemistry, biochemistry, biophysics, or related field required. Master’s degree in science preferred. - A minimum of 3 years of related research experience. - Strong background in biochemistry and molecular biology - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification) *Salary:* The budgeted salary range for the position is $48,000 to $60,000. The pay offered to the selected candidate will be determined based on factors including (but not limited to) the experience and qualifications of the selected candidate, including equivalent years in rank, training, and field or discipline; internal equity; and external market pay for comparable jobs. *About the University of Illinois Chicago* UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has over 300,000 alumni, and is one of the largest employers in the city of Chicago. Benefits eligible positions include a comprehensive benefits package which offers: Health, Dental, Vision, Life, Disability & AD&D insurance; a defined benefit pension plan; paid leaves such as Vacation, Holiday and Sick; tuition waivers for employees and dependents. Click for a complete list of *Employee Benefits <https://www.hr.uillinois.edu/benefits/>*. *Final authorization of the position is subject to availability of funding.* *UIC is an EOE including Disability/Vets.* *The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act* *The University of Illinois System requires candidates selected for hire to disclose any documented finding of sexual misconduct or sexual harassment and to authorize inquiries to current and former employers regarding findings of sexual misconduct or sexual harassment. For more information, visit **https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899 <https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899>*

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Deadline approaching: Integrative Structural Biology Summer School Padua Italy 7-11 July 2025
by Roberto Steiner 28 Apr '25

28 Apr '25

Dear All, Deadline is approaching for the International Summer School on “Current and Future Integrative Structural Biology”, taking place in the beautiful city of Padua, Italy, from 7–11 July 2025. Do not forget to register at the following link www.school2025.cristallografia.org<http://www.school2025.cristallografia.org/> This school will have a strong focus on cryo-EM, along with discussions on other cutting-edge techniques essential for modern structural biology research. Expert international speakers and tutors will provide valuable insights through lectures and practical sessions. With best wishes, Roberto (on behalf of the organising committee) Roberto A Steiner www.steinerlab.org<http://www.steinerlab.org> https://twitter.com/steiner_lab roberto.steiner(a)kcl.ac.uk<mailto:[email protected]> Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.steiner(a)unipd.it<mailto:[email protected]> Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours.

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Phenix Dock & Rebuild Python Error
by Nicholas Clark 22 Apr '25

22 Apr '25

Hi all, I'm trying to run Phenix Dock & Rebuild on a Mac (Venture 13.6.7) but I keep getting a NameError in Python that "DESKTOP_TYPE" is not defined. Does anyone have a quick way to fix this? Can I edit the code directly in that line to explicitly state that I'm on a mac or is this a variable that should be set directly in the base Python installation? Below is the entirety of the error message: NameError : global name 'DESKTOP_TYPE' is not defined Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Runtime.py", line 224, in OnComplete self.handle_complete_event(event) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Templates.py", line 491, in handle_complete_event self.add_result_panel(result) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Templates.py", line 512, in add_result_panel params=self.params) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Templates.py", line 980, in __init__ JobOutputPanel.__init__(self, parent) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Windows.py", line 551, in __init__ WidgetArea.__init__(self, parent) File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Windows.py", line 512, in __init__ self.DisplayWidgets() File "/Applications/phenix-1.20.1-4487/modules/phenix/wxGUI2/Programs/DockAndRebuild.py", line 112, in DisplayWidgets if (DESKTOP_TYPE in ['mac', 'kde', 'gnome']): NameError: global name 'DESKTOP_TYPE' is not defined Thanks! Best regards, Nick Clark

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Research Specialist Position at the University of Illinois to Study Ribosome Structure | POLIKANOV Lab
by Yury Polikanov 21 Apr '25

21 Apr '25

*Research Specialist Position Available, Department of Biological Sciences, University of Illinois at Chicago - Polikanov Lab* *The Polikanov Laboratory in the Department of Biological Sciences at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the Research Specialist position to study the structure and function of the bacterial ribosome.* For fullest consideration, please submit an application and cover letter describing your scientific interests and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group at https://uic.csod.com/ux/ats/careersite/1/home/requisition/7573?c=uic *Position Summary:* The research in the Polikanov Laboratory at UIC is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. This position is involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. Expected contributes to the design and delivery of research projects and collaborates with researchers to develop, execute, and interpret research projects. Performs complex laboratory and data collection techniques. *Duties & Responsibilities:* - Perform research relevant to the assigned projects; - Isolate, purify, and crystallize bacterial ribosomes; - Purify all additional components necessary for the crystallization experiments, such as recombinant proteins, tRNAs; - Collect X-ray diffraction data from the ribosome crystals at the APS and NSLS-II Synchrotrons; - Perform structural data analysis; - Coordinate, analyze, and document results for publication; - Directly participate in writing papers and grants based on the experimental data; - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry; - Attend weekly group meetings and journal club seminars. - Perform other related duties and participate in special projects as assigned. *Minimum Qualifications:* - A bachelor’s degree in chemistry, biochemistry, biophysics, or a related field is required. - A master’s degree in chemistry, biochemistry, biophysics, or a related field is preferred. - A minimum of 3 years related research experience. - Possesses and applies comprehensive knowledge of research principles, concepts, practices, and methods. - Proficient in standard molecular biology and biochemistry lab techniques, such as protein expression, and purification *Preferred Qualifications:* - Experience in structural biology (cryo-EM or X-ray crystallography); - Experience in RNA biology, ribosome, and/or protein synthesis fields. *About the University of Illinois Chicago:* UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has nearly 260,000 alumni, and is one of the largest employers in the city of Chicago. *The University of Illinois System is an equal opportunity employer, including but not limited to disability and/or veteran status, and complies with all applicable state and federal employment mandates. Please visit Required Employment Notices and Posters <https://www.hr.uillinois.edu/cms/one.aspx?portalId=4292&pageId=5705> to view our non-discrimination statement and find additional information about required background checks, sexual harassment/misconduct disclosures, COVID-19 vaccination requirement, and employment eligibility review through E-Verify. **The university provides accommodations to applicants and employees. Request an Accommodation <https://jobs.uic.edu/request-and-accomodation/>*

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sub-unitary occupancy group restraints sum
by Kreitler, Dale 17 Apr '25

17 Apr '25

Hi, For refining an x-ray structure which has a ligand bound with multiple poses modeled as alternate confirmations, is there a way in phenix refine to maintain that the occupancy of each conformation is equal while allowing the sum total occupancy to vary (rather than equal 1)? I realize the [0,1] min/max occupancy values are adjustable parameters -- my interpretation of the docs is that this is not possible, but I thought it'd be worth asking. An example might be a ligand bound with partial occupancy near a rotational symmetry axis. Thank you, Dale ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318

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twinning and translational NCS issues
by Wenhui Xi 16 Apr '25

16 Apr '25

Hi all, i have this crystal which was reported severe issues with twinning and translational NCS, thus when i tried to refine its structure, the Rfree would go up to nearly 60% which making directly solving its structure very hard. i'm writing to ask are there any helpful ways to deal with this issue? Thank you! Joyce [image: image.png]

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CBMS Structural Biology Workbench - May 27 through 30, 2025 - registration deadline April 15
by Stojanoff, Vivian 14 Apr '25

14 Apr '25

Dear Colleagues, The CBMS Structural Biology Workbench will take place May 27 through 30, 2025. The first two days, May 27 and 28, are dedicated to MX and the following days May 29 and 30 to Solution Scattering and X-ray Footprintig. This is an IN-PERSON workshop. DEADLINE to REGISTER APRIL 15 https://www.bnl.gov/cbmsworkbench/ PROGRAM Macromolecular Crystallography May 27 - MX data collection on participants samples and pre-analysis May 28 - Phenix workshop "The Phenix workshop will focus on crystallographic refinement using phenix.refine. The first lecture will introduce major features and best practices of reciprocal space refinement, followed by a basic tutorial demonstrating how to run phenix.refine with default options. The second lecture will cover strategies for low-resolution refinement, including the use of secondary structure restraints and reference models. Participants who so desire will have the opportunity to work on their own data with Phenix developers available to answer questions—on phenix.refine or any other Phenix tools in the afternoon. Solution Scattering - SAXS & Xray Footprinting - XFP May 29 - Introduction to SAXS & LIX; Data collection on participants samples May 30 morning - SAXS data analysis software May 30 afternoon - Introduction to XFP and hands-on tutorial Questions can be directed to Vivian Stojanoff (stojanof(a)bnl.gov). ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?…>

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Re: phenixbb Digest, Vol 232, Issue 13 (out of office)
by Elisabeth Laurent 13 Apr '25

13 Apr '25

Thank you for your e-mail. I am out of office until April 23rd, 2025. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: bmca(a)boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 13.4.25 20:51 >>> Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: Question about geometry outliers in RealSpaceRefine (Pavel Afonine) 2. Re: DEN restraints and ECHT disorder models (Tom Burnley - STFC UKRI) ---------------------------------------------------------------------- Message: 1 Date: Fri, 11 Apr 2025 11:47:11 -0700 From: Pavel Afonine <pafonine(a)lbl.gov> Subject: [phenixbb] Re: Question about geometry outliers in RealSpaceRefine To: Kevin M Jude <kjude(a)stanford.edu>, "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Message-ID: <7968370b-7470-4fe4-aaf1-052661202ef9(a)lbl.gov> Content-Type: multipart/alternative; boundary="------------YozFq5Oyt0xmhpmEfOqMdIo0" Hi Kevin, could you please send me the file (off list)? Thanks! Pavel On 4/11/25 09:34, Kevin M Jude wrote: > > After a recent RealSpaceRefine run, the Geometry Restraints tab in the > gui reports that I have two bond angle outliers > 4 sigma, but only > lists one of them: > > D 180 MET N, D 180 MET CA, D 180 MET CB 114.170 109.342 4.2 > > So I check the logfile for the job and see: > > Bond angle restraints: 12582 > > Sorted by residual: > > angle pdb=" N MET D 180 " > > pdb=" CA MET D 180 " > > pdb=" CB MET D 180 " > > ideal model delta sigma weight residual > > 114.17 109.34 4.83 1.14e+00 7.69e-01 1.79e+01 > > angle pdb=" CA LEU B 79 " > > pdb=" CB LEU B 79 " > > pdb=" CG LEU B 79 " > > ideal model delta sigma weight residual > > 116.30 127.81 -11.51 3.50e+00 8.16e-02 1.08e+01 > > angle pdb=" C ASP B 333 " > > pdb=" N SER B 334 " > > pdb=" CA SER B 334 " > > ideal model delta sigma weight residual > > 122.74 127.19 -4.45 1.44e+00 4.82e-01 9.54e+00 > > angle pdb=" C GLN D 167 " > > pdb=" N ARG D 168 " > > pdb=" CA ARG D 168 " > > ideal model delta sigma weight residual > > 121.48 126.80 -5.32 2.04e+00 2.40e-01 6.80e+00 > > angle pdb=" C ASP B 163 " > > pdb=" N THR B 164 " > > pdb=" CA THR B 164 " > > ideal model delta sigma weight residual > > 123.47 127.30 -3.83 1.53e+00 4.27e-01 6.27e+00 > > ValidationCryoEM returns identical results except the gui says only > one > 4-sigma outlier (at //D/Met180/). PDB Validation reports only > the outlier at //B/Leu79/, which does have the largest sigma in the > above log. > > My questions are: > > 1. Why does the gui report two 4-sigma outliers but only show one? > 2. Why do the sigmas in the log file not correspond to the sigmas in > the gui? > > Best wishes > > Kevin > > -- > > Kevin Jude, PhD > > Structural Biology Research Specialist, Garcia Lab > > Howard Hughes Medical Institute > > Stanford University School of Medicine > > Beckman B177, 279 Campus Drive, Stanford CA 94305 > > > _______________________________________________ > phenixbb mailing list --phenixbb(a)phenix-online.org > To unsubscribe send an email tophenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s

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DEN restraints and ECHT disorder models
by Roberto Battistutta 13 Apr '25

13 Apr '25

Dear all, From which version of Phenix are the DEN restraints and ECHT disorder models implemented in the ensemble refinement (as described in Ploscariu, N., Burnley, T., Gros, P. & Pearce, N. M. (2021). Improving sampling of crystallographic disorder in ensemble refinement. Acta Cryst. D77, 1357-1364)? Thank you very much, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistutta(a)unipd.it

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Question about geometry outliers in RealSpaceRefine
by Kevin M Jude 11 Apr '25

11 Apr '25

After a recent RealSpaceRefine run, the Geometry Restraints tab in the gui reports that I have two bond angle outliers > 4 sigma, but only lists one of them: D 180 MET N, D 180 MET CA, D 180 MET CB 114.170 109.342 4.2 So I check the logfile for the job and see: Bond angle restraints: 12582 Sorted by residual: angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 114.17 109.34 4.83 1.14e+00 7.69e-01 1.79e+01 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 127.81 -11.51 3.50e+00 8.16e-02 1.08e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 127.19 -4.45 1.44e+00 4.82e-01 9.54e+00 angle pdb=" C GLN D 167 " pdb=" N ARG D 168 " pdb=" CA ARG D 168 " ideal model delta sigma weight residual 121.48 126.80 -5.32 2.04e+00 2.40e-01 6.80e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 127.30 -3.83 1.53e+00 4.27e-01 6.27e+00 ValidationCryoEM returns identical results except the gui says only one > 4-sigma outlier (at //D/Met180/). PDB Validation reports only the outlier at //B/Leu79/, which does have the largest sigma in the above log. My questions are: 1. Why does the gui report two 4-sigma outliers but only show one? 2. Why do the sigmas in the log file not correspond to the sigmas in the gui? Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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Simulate map from model
by Ricardo Righetto 09 Apr '25

09 Apr '25

Hi, Apologies if I'm missing something obvious, but I was not able to find this in the documentation: is there a PHENIX tool for simulating Coulomb potential maps (aka "cryo-EM maps") from atomic models? I'm looking for something like the molmap <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> command in ChimeraX, but more accurate. One such alternative is the simulate program from cisTEM, but I figured PHENIX might also have something? Thank you! -- Ricardo Diogo Righetto

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Differential density peaks and hydrophobic residues
by Lucas Souza 04 Apr '25

04 Apr '25

Hi everyone, I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied). Does anyone have a guess about that? Best, Lucas -- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000

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CBMS Structural Biology Workbench - May 27 through 30, 2025 - registration deadline approaching
by Stojanoff, Vivian 03 Apr '25

03 Apr '25

Dear Colleagues, The CBMS Structural Biology Workbench will take place May 27 through 30, 2025. The first two days, May 27 and 28, are dedicated to MX and the following days May 29 and 30 to Solution Scattering and X-ray Footprintig. This is an IN-PERSON workshop. DEADLINE to REGISTER APRIL 15 https://www.bnl.gov/cbmsworkbench/ PROGRAM Macromolecular Crystallography May 27 - MX data collection on participants samples and pre-analysis May 28 - Phenix workshop "The Phenix workshop will focus on crystallographic refinement using phenix.refine. The first lecture will introduce major features and best practices of reciprocal space refinement, followed by a basic tutorial demonstrating how to run phenix.refine with default options. The second lecture will cover strategies for low-resolution refinement, including the use of secondary structure restraints and reference models. Participants who so desire will have the opportunity to work on their own data with Phenix developers available to answer questions—on phenix.refine or any other Phenix tools in the afternoon. Solution Scattering - SAXS & Xray Footprinting - XFP May 29 - Introduction to SAXS & LIX; Data collection on participants samples May 30 morning - SAXS data analysis software May 30 afternoon - Introduction to XFP and hands-on tutorial Questions can be directed to Vivian Stojanoff (stojanof(a)bnl.gov).

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for autobuild full sequence?
by James Holton 03 Apr '25

03 Apr '25

Hey all, Don't worry, nothing is funny today. I have a real question: Is there a way to force phenix.autobuild to build in the entire sequence? As in: the full length of the actual molecule that is in the crystal, such as what is supposed to go into SEQRES, regardless of "visible" density? I am trying to come up with a pipeline for prepping MD simulations of protein crystals. It seems proper to me that the molecule being simulated should be the actual molecular species, disordered bits an all. However, we don't seem to have good technology for building protein chains into "nothingness". Yes, I know Alphafold is a thing, but it is rubbish at clashes in the context of a crystal. I mean, I could write something, but does this tool already exist? Cheers, and happy Tuesday, -James Holton MAD Scientist

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CloudFlare and Spain
by Billy Poon 31 Mar '25

31 Mar '25

Hi everyone, Does anyone in Spain have issues reaching the Phenix website ( https://phenix-online.org)? Our website is behind CloudFlare and it looks like, periodically, some CloudFlare IP addresses are blocked in Spain due to some piracy issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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IBA2025 - May 5&6 2025 - Cambridge MA
by Chip Lesburg 30 Mar '25

30 Mar '25

The Industrial Biostructures America conference will take place on May 5 & 6, 2025 at the MassBioHub in Cambridge MA. The conference was launched in 2018 to bring the industry-based structural biology community together for two days of presentations and networking. This is a great place for industrial structural biologists, as well as those who are industry-curious. The conference will feature keynote presentations by: * Dr. Stephen K. Burley, Director RCSB Protein Data Bank and Rutgers University Professor * Dr. James Fraser, Professor and Chair Department of Bioengineering and Therapeutics Sciences at UCSF * Dr. Stephen Harrison, Professor Harvard Medical School/Investigator Howard Hughes Medical Institute * Dr. Mark Murcko, Founding CSO/Board Member at Dewpoint Therapeutics and Relay Therapeutics Conference information is available at https://industrialbiostructuresamerica.org along with guidelines for submitting abstracts for scientific presentations during the conference. Scientific sessions will cover the following topics: * Structural Biology of Targeted Protein Degradation: Glues, TCs & DUBs * Developing Fragments to Drugs: Challenges & Victories * Molecular Dynamics and Allostery - Bridging Experimental and Computational Drug Discovery * Membrane Protein Structure Guided Design * CryoEM Synergies with Molecular Modeling and Computational Models * Biologics (Antibody Design & ADCs) * AI/ML in Structural Biology and Drug Discovery * Hot Topics (SBDD, Kinases, RNA) The abstract deadline is April 1. Space is limited so if you're interested, please register soon. Contact us at iba(a)proteros.com<mailto:[email protected]> for information regarding Exhibitor and Sponsor opportunities [cid:logo_c70edd4a-e7f0-4d54-be6f-d03f53f0c961.png] Charles Lesburg Vice President, Structural Biology odysseytx.com<https://protect.checkpoint.com/v2/___https:/odysseytx.com/___.YzJ1Om9keXNzZ…> This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender.

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can not launch phenix gui
by lzhlizehou＠outlook.com 29 Mar '25

29 Mar '25

Dears, I am using Ubuntu 24.04 and have successfully installed phenix-1.21.2-5419. However, when I attempt to launch the GUI by running the phenix command, it fails with the following error: Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 961, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/usr/local/phenix-1.21.2-5419/build/../modules/phenix/wxGUI2/command_line/main.py", line 34, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.21.2-5419/build/../modules/phenix/wxGUI2/command_line/main.py", line 28, in run wxapp = App.PhenixApp(args) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 84, in __init__ wx.App.__init__(self, 0) File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 118, in OnInit show_splash_screen(timeout=2000) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 1015, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. Looking forward to your reply. Best regards Li

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Call for Abstracts - Combining experimental data with predicted models - Session at the ACA Meeting, July 18-23, 2025
by Christopher Williams 24 Mar '25

24 Mar '25

Dear All, Rakhi Rajan and I are co-chairing the session "Combining experimental data with predicted models for structure determination" session at the 75th American Crystallographic Association Meeting in Lombard, IL (near Chicago) from July 18–23, 2025. It's a great meeting, and we encourage both general attendance and submissions for our session. We welcome abstract submissions for both talks and posters. If you're interested, please submit your abstract at https://www.acameeting2025.com/. Deadlines are fast approaching: March 31 – Deadline for oral abstracts & travel grant applications April 30 – Deadline for poster abstracts We invite contributions of novel methods and pipelines for combining prediction and experiment. We also invite stories of working with predictions and data. Have you gotten into the weeds with AlphaFold? Has structure prediction let you better design an experiment? Or has experimental data revealed an important detail missing from prediction? We want to hear about it! If you're interested in sponsoring our session, please reach out as well. -Christopher Williams ---Richardson Lab, Duke University -Rakhi Rajan ---University of Oklahoma

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Issues with zero B-factor and ADP refinement
by sylee00＠snu.ac.kr 23 Mar '25

23 Mar '25

Dear all, I am encountering issues related to B-factors and ADP refinement in Phenix and would appreciate any insights or suggestions. I am currently working on my first PDB file, but I've noticed that many atoms in the PDB file have a B-factor of 0. As far as I understand, B-factor values are calculated by ADP refinement in Phenix real-space refinement, but even after running real-space refinement (with ADP on in refinement settings), the B-factor remains 0 for many atoms. I am currently using Phenix 1.20 on Windows (Newest version available on window). I also attempted to run Phenix 1.21 on a Linux in other computer, but when ADP refinement is enabled, the process starts normally but halts during the ADP refinement step. So I couldn't test whether the issue is fixed in the newest version. Aside from the B-factor issue, I am also experiencing an inssue related to ADP refinement: When I run real-space refinement with ADP refinement enabled, the process starts normally but halts during the ADP refinement step. According to the log file, other refinement steps proceed without issues, but it fails to progress at the ADP refinement stage. Additionally, when I try to pause the process, I receive a "NoSuchProcess" error, so ADP refinement process may have unexpectedly terminated. At first, I thought it's the issue related to system performance or hardware differences, because adp refinement with this pdb file and identical parameters works on some computer but fails on others (the same version of Phenix). Still it's weird because this issue has occurred unexpectedly, as ADP refinement previously worked in my computer under the same conditions without any problems and also other PDB files run without any problems in my computer. I would appreciate any insights or suggestions on how to resolve this. Thanks

3 3

phenix low resolution refinement strategies
by a131943017＠163.com 20 Mar '25

20 Mar '25

Hi, how do I set the optimization parameters to make free R lower for 3.2Å x-ray crystallography data, or in other words, how do I go about determining whether the optimization strategy is appropriate or not? Questions from a Phenix Beginner.

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seeking help for phenix - coot model building
by tim smith 20 Mar '25

20 Mar '25

Hi everyone, I’m currently working on building a model and have encountered some difficulties with the map-model process. I would greatly appreciate it if anyone could assist me in either helping to build the model or teaching me how to do it. I’m happy to offer a suitable reward for your time and help. Thank you in advance for considering! Regards, Stim

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CSD changes conformation to planar during phenix.refine
by Andrea Smith 20 Mar '25

20 Mar '25

Hi all, I have a structure where I clearly see that one of the cysteines is oxidised. I have modelled CSD instead of CYS and when I do real space refine in Coot, the CSD sits nicely in the density. When I submit the phenix.refine job, I can see that the geometry changes and now the SOOH is planar. I tried to add the CSD.cif from PDB into phenix.refine as restraints, but it doesn't help and during the automatic refinement the geometry is changed to planar again. Anyone experienced same thing? What do I do? Thank you, Andrea

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Trouble with GTP/GDP refinement.
by DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO 18 Mar '25

18 Mar '25

Dear phenixbb: I'm working with a GTP binding protein and have had some problems running phenix_refine. In my unit cell there are two molecules one with GDP and one with GTP, which I added in Coot(0.9.8). When refining the following error message pops-up : "Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols:4 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modifications and apply_cif_link parameter definitions if necessary". Checking the log file I found that the problem seems to be hydrogen atoms from these ligands Number of atoms with unknown nonbonded energy type symbols: 4 "HETATM 6499 H5' GTP A 501 .*. H " "HETATM 6502 H5'' GTP A 501 .*. H " "HETATM12939 H5' GDP B 501 .*. H " "HETATM12940 H5'' GDP B 501 .*. H " Including the corresponding .CIF files (dowloaded from PDB) did not solve the problem and the same error popped. Since I'm in the initial stages of the refinement I'm running phenix with bindividuals. Could anybody save my day giving me some light into this issue? Cheers, Diego

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.cif file has 'UNK' auth_asym_id
by Kevin M Jude 14 Mar '25

14 Mar '25

I’ve finished refining a structure with three protein chains A, B, C. The pdb file looks ‘normal’ to me, but when I inspect the .cif file written by phenix, the auth_asym_id for chains B and C is ‘UNK’. label_asym_id is correct for all chains. I’m not really sure what the difference is between the auth_ and label_ fields. When I try to perform actions on the .cif file, I get duplicate atom label errors. Here’s a few example lines from the .pdb and .cif files, where auth_asym_id is field 6 and label_asym_id is field 16 ATOM 460 OXT PRO A 59 5.272 55.689 31.481 1.00 52.63 O ANISOU 460 OXT PRO A 59 6541 6212 7244 1448 1260 96 O TER ATOM 461 N ALA B 2 39.292 61.974 39.403 1.00 67.81 N ANISOU 461 N ALA B 2 7118 8729 9916 -1711 -388 2066 N ATOM 460 OXT . PRO A 59 ? 5.27169 55.68852 31.48123 1.000 52.63052 O ? A ? 58 1 ATOM 461 N . ALA UNK 2 ? 39.29207 61.97430 39.40271 1.000 67.80544 N ? B ? 1 1 I’m able to convert the pdb file to a usable cif file using gemmi but wanted to report this weird behavior with phenix 1.21.2_5419. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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Pdb validation report via phenix
by Stachowski, Tim 12 Mar '25

12 Mar '25

I’ve always found the phenix.get_pdb_validation tool to be super helpful to gauge where my refinements are relative to the PDB, especially since I work mainly through the command line. But sometime around late last year, the R-free metric stopped being calculated (probably related to “EDS: FAILED”). Is there a way to bring this part of the tool back – or does anyone have a work around they can share? I’m running the command like: phenix.get_pdb_validation_report final-coot-3_refine_001.reflections.cif final-coot-3_refine_001.cif with version: phenix-2.0rc1-5599 Thanks Tim -- Tim Stachowski, PhD St. Jude Children’s Research Hospital ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

2 1

Refining the structure of Ribosome and the system crash
by Rajnandani Kashyap 12 Mar '25

12 Mar '25

Hello Everyone I am trying to run jobs in phenix (real space refinement alignment with the other modelling jobs), but the system always crashes, and refinement doesn't complete. This is the structure of ribosome, and I am wondering what to do to get through the refinement. Is there any specific parameters I should be using. I tried to change the processors to 15 for a 20-processor computer. Let me know. Thanks in advance. FYI: There is no error message in the log. Best, Rajnandani ---------------------------------------------------------------------- Rajnandani Kashyap, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology Saint Louis University, Antony Lab 1205 Carr Lane, DRC 451 St. Louis, MO 63104 https://orcid.org/0000-0002-9141-1168 -----------------------------------------------------------------------

1 0

Ion placement (anomalous) + occupancy refinement
by miha.pavsic＠fkkt.uni-lj.si 06 Mar '25

06 Mar '25

Hi everyone, I have a dataset from a protein that contains 2 Ca2+ binding sites. The Ca2+ loaded protein was crystallized in the presence of Tb3+ which at one site mostly replaced Ca2+, however at the other site the Tb3+/Ca2+ ratio appears to be much lower (judging from anomalous map; data collected at 1.3 Å wavelength, MR for phasing). The occupancy sum of Tb3+ and Ca2+ at each of the two sites is strongly believed to be 1. While I am aware of the ion placement option in phenix.refine, I am not so sure how to refine the partial occupancies using anomalous data, if possible. Many thanks for any hints, Miha

3 2

AKM in Phenix
by lucas.santosouza＠outlook.com 06 Mar '25

06 Mar '25

Hi everyone, Is there still support for the generation of Average Kick Maps in Phenix? I am using both versions 1.21.2-5419 and the nightly build 2.0rc1-5555. I added kicked=True to the maps.params, but phenix.maps gives me "Unused parameter definitions: maps.map_coefficients.kicked (file "maps.params", line 53)". I also cannot see the "Kicked map" check box in the Create Maps GUI. Cheers, Lucas

2 1

Refine partially occupied ligand in active site containing chloride ions
by Stephen.carr＠rc-harwell.ac.uk 06 Mar '25

06 Mar '25

Dear phenix bb, I am trying to refine a ligand in the active site of my protein where the ligand occupancy is ~50%. The empty active site contains two chloride ions and the residual density from these ions is very prominent when the model is refined with the ligand alone. I would like to refine the model with both the ligand and chloride ions present and have been trying to do this with altLoc flags but so far with no luck. I'm assuming that since the Cl ions more-or-less directly overlay atoms from the ligand positional refinement keeps pushing them out of the density. I'm sure there is a simple way to get around this and I would be grateful for any suggestions. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.carr(a)rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.

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Program crash
by F.Xavier Gomis-Rüth 05 Mar '25

05 Mar '25

Dear all, I recently upgraded my MacOS to Sequoia 15.3.1 and found that previous phenix jobs that ran without problem suddenly crashed with the installation (phenix-1-21.2-5419) I had since August 2024. So I installed the latest on-built (phenix-2.0rc-5617) but it nonetheless crashed with the message below. Any help would be greatly appreciated. Best, Xavier XGRMAC:cyc3 > Could not import the compiled Python-sander interface.Traceback (most recent call last): File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 8, in <module> run_program(real_space_refine.Program) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/iotbx/cli_parser.py", line 980, in run_program task.run() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1524, in energies_sites pair_proxies = self.pair_proxies( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7151 > 50: distance: 0 - 1: 15.382 distance: 1 - 2: 14.133 distance: 1 - 3: 15.077 distance: 4 - 5: 11.010 distance: 5 - 6: 5.064 distance: 5 - 8: 12.166 distance: 6 - 7: 9.252 distance: 6 - 15: 4.656 distance: 8 - 9: 6.568 distance: 9 - 10: 41.112 distance: 9 - 11: 19.959 distance: 10 - 12: 4.365 distance: 11 - 13: 12.611 distance: 12 - 14: 28.654 distance: 13 - 14: 25.314 distance: 15 - 16: 7.291 distance: 16 - 17: 12.341 distance: 16 - 19: 4.354 distance: 17 - 18: 11.820 distance: 17 - 26: 9.661 distance: 19 - 20: 7.438 distance: 20 - 21: 17.074 distance: 20 - 22: 19.126 distance: 21 - 23: 7.637 distance: 22 - 24: 3.434 distance: 23 - 25: 24.169 distance: 24 - 25: 8.875 distance: 26 - 27: 10.037 distance: 27 - 28: 9.377 distance: 27 - 30: 12.844 distance: 28 - 29: 12.437 distance: 28 - 34: 22.926 distance: 30 - 31: 46.409 distance: 31 - 32: 6.849 distance: 31 - 33: 21.459 distance: 34 - 35: 12.375 distance: 34 - 40: 15.635 distance: 35 - 36: 10.511 distance: 35 - 38: 12.461 distance: 36 - 37: 11.525 distance: 36 - 41: 15.668 distance: 38 - 39: 9.083 distance: 39 - 40: 10.922 distance: 41 - 42: 15.925 distance: 42 - 43: 26.537 distance: 42 - 45: 20.600 distance: 43 - 44: 14.038 distance: 43 - 48: 40.043 distance: 45 - 46: 18.721 distance: 45 - 47: 12.152 distance: 48 - 49: 19.936 distance: 49 - 50: 9.210 distance: 49 - 52: 4.170 distance: 50 - 51: 6.051 distance: 50 - 56: 10.707 distance: 52 - 53: 13.486 distance: 53 - 54: 25.122 distance: 53 - 55: 30.977 distance: 56 - 57: 24.676 distance: 57 - 58: 6.469 distance: 57 - 60: 24.810 distance: 58 - 59: 19.649 distance: 58 - 65: 16.713 distance: 60 - 61: 19.749 distance: 61 - 62: 27.563 distance: 62 - 63: 31.258 distance: 63 - 64: 39.081 distance: 65 - 66: 17.034 distance: 66 - 67: 13.877 distance: 66 - 69: 30.087 distance: 67 - 68: 30.739 distance: 67 - 70: 22.852 distance: 70 - 71: 17.537 distance: 71 - 72: 19.009 distance: 71 - 74: 23.249 distance: 72 - 73: 32.627 distance: 72 - 81: 23.614 distance: 74 - 75: 30.150 distance: 75 - 76: 11.440 distance: 75 - 77: 13.841 distance: 76 - 78: 23.906 distance: 77 - 79: 27.669 distance: 78 - 80: 29.196 distance: 79 - 80: 27.009 --

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Cryo_fit installation
by omar.debei＠unipr.it 28 Feb '25

28 Feb '25

Hi everyone, I was wondering if you could help me with installing cryo_fit on an Ubuntu machine. I followed the instructions here for the cryo_fit installation. Then, I tried to follow this guide to install gromacs_cryo_fit. However, I got stuck at the "Install using a provided script" step. Do I need to install GROMACS separately before proceeding? Any tips would be greatly appreciated! Many thanks, Omar

2 2

Register by Feb. 28th for the West Coast Structural Biology Workshop
by Michael Thompson 21 Feb '25

21 Feb '25

The registration and abstract submission deadlines for the 26th West Coast Structural Biology Workshop are just one week away... Register today, and be a part of this iconic meeting with over 50 years of tradition!! See below for a message about the conference: Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025. The meeting is scheduled for March 23-26, 2025 at its traditional location, the Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is February 28, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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Postdoc and PhD positions in quantum/protein/electron crystallography. Application deadline March 2nd
by Paulina Dominiak 03 Feb '25

03 Feb '25

Dear Colleagues, We currently have several positions available in my group at the University of Warsaw - both postdoc and PhD. The research project combines quantum crystallography with protein crystallography, focusing on 3DED/microED techniques. We're interested in hearing from researchers with different backgrounds: * Software developers who want to learn crystallography * Protein crystallographers looking to expand their skills * Small-molecule crystallographers experienced with X-ray charge density studies * Researchers familiar with electron crystallography Detailed information about the positions, project description, and application links can be found at: http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/ <http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/> Application deadline: March 2nd, 2025 Please share this opportunity with qualified candidates who might be interested. For additional information, feel free to contact me directly. Best regards, Paulina -- Prof. dr hab. Paulina M. Dominiak Group Leader Electron Density Modelling Group Laboratory for Structural and Biochemical Research (LBSBio) Biological and Chemical Research Centre Department of Chemistry University of Warsaw ul. Zwirki i Wigury 101 02-089 Warszawa, Poland Room: 3.125 E-mail:[email protected] Phone: (48) 22 55 26 714 WWW:http://4xeden.uw.edu.pl

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DEADLINE EXTENDED: 26th West Coast Structural Biology Workshop
by Michael Thompson 03 Feb '25

03 Feb '25

Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025 and Feb. 21, 2025 respectively. The meeting is scheduled for March 23-26, 2025 at its traditional location, the Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is February 21, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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Re: Uknown non bonded
by Yann Lefrançois.C 30 Jan '25

30 Jan '25

Hi thank you for your reply, I'm not working with ligand, but a complexe. I do not have hydrogen in my model, so it seems I have a bigger problem. [image: image.png] I tried to use PDB_REDO, however i'm using mrc format for my ED map Le jeu. 30 janv. 2025 à 16:39, Georg Mlynek <georg.mlynek(a)univie.ac.at> a écrit : > Hi Yann, can you post a screenshot of the error message? It should be > stated there which are causing problems. > > Very often the problems are hydrogens. So just delete those. One easy > way is to do is to open in coot and when saving there is a tick box > without hydrogens. There are also tools in phenix doing this. > > Also you can submit the pdb to PDB_REDO to check if there are more sever > problems. If PDB_REDO runs then there are no big errors. Then just use > the output for phenix refine. > > And as Xavier wrote ligands also can cause problems. But also there most > times the hydrogens. > > Br, Georg. > > > Am 2025-01-30 um 4:26 PM schrieb yannlefrancoiscopy(a)gmail.com: > > Hello, > > I'm a newbie phenix user, and i was trying to refine a model. > > > > and when i tried to refine it, I got an error message saying that some > atoms had unknown nonbonded interaction. > > > > However, there are no indication to which one are problematic, Any tips > on how to find the problematic one and how to correct them ? > > > > best wishes, > > Yann > > _______________________________________________ > > phenixbb mailing list -- phenixbb(a)phenix-online.org > > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > > Unsubscribe: phenixbb-leave@%(host_name)s >

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Uknown non bonded
by yannlefrancoiscopy＠gmail.com 30 Jan '25

30 Jan '25

Hello, I'm a newbie phenix user, and i was trying to refine a model. and when i tried to refine it, I got an error message saying that some atoms had unknown nonbonded interaction. However, there are no indication to which one are problematic, Any tips on how to find the problematic one and how to correct them ? best wishes, Yann

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open position for a 2(+2) year postdoc working on plant sugar and hormone transport at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 29 Jan '25

29 Jan '25

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in biophysical and structural characterization of sugar and hormone transport, Denmark online posting: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral… We are looking for a highly skilled and motivated postdoc with an interest in working on sugar and hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from spring 2025, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to a total of 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of sugar and hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Schulz & Ung et al. "Transport of herbicides by PIN-FORMED auxin transporters" bioRxiv (2024) Andersen et al. Basis of Glucose and Fructose Selectivity in Sugar Transport Proteins" bioRxiv (2024) Bavnhøj et al. “Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter.” Nature Plants 7 (2023) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 28. Feb. 2025 using the online application system (link above).

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Reminder: Phenix Postdoc Position - Berkeley, California
by Paul Adams 27 Jan '25

27 Jan '25

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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About d99
by Roberto Battistutta 24 Jan '25

24 Jan '25

Dear Phenix people, In "New tools for the analysis and validation of cryo-EM maps and atomic models” (ActaD 2018), it is reported that "map sharpening can affect d99 (Fig. 9g) but it is rather insensitive to masking (Fig. 9h).” I have a case where d99 increases a lot with masking, as shown in the screenshot below (from Mtriage). On the other hand, FSC decreases. What does this mean? Can it be attributed to the fact that there is a strong scatterer in the molecule (a heavy atom) that strongly influences the intensity of the map? Are there other possible explanations (preferential orientation for example)? What is the best way to handle such maps? Thank you for the attention. Best, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistutta(a)unipd.it

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André Mitschler, former crystallography engineer in the BSI department, Strasbourg
by Alexandre OURJOUMTSEV 24 Jan '25

24 Jan '25

Sorry, my previous e-mail left with a wrong subject… Sacha = = = = Dear all, for those (I expect, many of you) who knew André Mitschler, I resubmit the message below. Sad news. It was a great and non-trivial person. With best wishes, Sacha Urzhumtsev = = = = From: Valerie LAMOUR <lamourv(a)igbmc.fr<mailto:[email protected]>> Sent: Friday, January 24, 2025 4:23 PM Subject: André Mitschler, former crystallography engineer in the BSI department André Mitschler est décédé le 5 Décembre, à l’âge de 83 ans. André était un cristallographe expérimental hors pair. Il a débuté en recherche dans le laboratoire du Prof Weiss où il a eu la charge du premier diffractomètre à RX de l’époque. En 1967, a entamé une fructueuse collaboration avec Dino Moras qui a pu bénéficier de son expertise et son adresse expérimentale pour sa thèse de 3e cycle. Leurs liens ne se sont jamais rompus. En 1981 Il a rejoint le laboratoire de cristallographie de Dino, nouvellement créé à l’IBMC. Il y a effectué le reste d’une fructueuse carrière d’ingénieur CNRS qui, en 1994, s’est poursuivie à l’IGBMC, un nouvel institut créé à Illkirch avec un important soutien de l’industrie pharmaceutique. En 1996, il a rejoint le groupe d’Alberto Podjarny, pour travailler dans la détermination de la structure de l’Aldose Reductase humaine. Les cristaux diffractaient à une résolution extrêmement haute (0.6 Angstroms). La mesure des données a demandé des nouveaux développements et l’utilisation des meilleures lignes synchrotron du monde. André était à la hauteur du défi, avec la capacité de passer de longues heures à monter et tester expérimentalement des cristaux. Il pouvait travailler 72 heures d’affilée dans le synchrotron d'Argonne National Lab. Le travail a culminé en 2008, avec la publication d’un mécanisme enzymatique inattendu. En 1999, il a obtenu la médaille de Cristal du CNRS, en reconnaissance de ses travaux en cristallographie expérimentale. André était aussi un passionné de l’histoire militaire, et a fait une carrière dans l’armée jusqu’à rang de colonel dans la cavalerie. Sa passion par la recherche, sa force de travail et son dévouement pour l’excellence expérimentale sont un exemple à suivre par tous les jeunes chercheurs. //// André Mitschler passed away on December 5th at the age of 83. André was an outstanding experimental crystallographer. He began his research career in Professor Weiss's laboratory, where he was responsible for the first X-ray diffractometer at the time. In 1967, he started a fruitful collaboration with Dino Moras, whose doctoral work benefited greatly from André's expertise and experimental skill. Their professional ties endured throughout their lives. In 1981, André joined Dino’s newly established crystallography laboratory at IBMC, where he spent the remainder of a productive career as a CNRS engineer. In 1994, he continued his work at IGBMC, a new institute in Illkirch supported by the pharmaceutical industry. In 1996, André joined Alberto Podjarny’s group to work on determining the structure of human aldose reductase. The crystals diffracted at an exceptionally high resolution (0.6 Å), which required innovative developments and access to the world's most advanced synchrotron beamlines. André rose to the challenge, demonstrating his ability to spend long hours preparing and experimentally testing crystals. He worked tirelessly, including 72-hour shifts at the Argonne National Laboratory synchrotron. This effort culminated in 2008 with the publication of an unexpected enzymatic mechanism. In 1999, André was awarded the CNRS Crystal Medal in recognition of his contributions to experimental crystallography. André was also a military history enthusiast and pursued a parallel career in the army, rising to the rank of colonel in the cavalry. His passion for research, tireless work ethic, and dedication to experimental excellence remain an inspiration for young researchers.

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Phenix Postdoc Position - Berkeley, California
by Paul Adams 24 Jan '25

24 Jan '25

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Error in Windows installation: Phenix 1.21.2-54
by Jobichen Chacko 18 Jan '25

18 Jan '25

ImportError : __import__("gltbx_glu_ext"): DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. sys.path: C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\libsvm C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\phenix\wxGUI2\command_line C:\ProgramData\phenix-1.21.2-5419\python39.zip C:\ProgramData\phenix-1.21.2-5419\DLLs C:\ProgramData\phenix-1.21.2-5419\lib C:\ProgramData\phenix-1.21.2-5419 C:\ProgramData\phenix-1.21.2-5419\lib\site-packages C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\mmtbx\suitename Traceback (most recent call last): File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\boost_adaptbx\boost\python.py", line 22, in import_ext try: mod = __import__(name) ImportError: DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\MainWindow.py", line 745, in <lambda> menu.add_command("Run now", lambda evt: self.run()) File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Main.py", line 426, in run self.start_process(config_file, output_dir, process_type) File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Templates.py", line 701, in start_process run_notebook = self.create_run_notebook() File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Main.py", line 532, in create_run_notebook from wxGUI2.Programs.Refine import Output File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\Programs\Refine\Output.py", line 5, in <module> from wxGUI2 import GLViewer, AdvancedWidgets, Buttons File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\wxGUI2\GLViewer.py", line 10, in <module> from crys3d.wx_combined_viewer import viewer_phil File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_combined_viewer.py", line 4, in <module> from crys3d.wx_selection_editor import selection_editor_mixin File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_selection_editor.py", line 6, in <module> from crys3d.wx_model_viewer import model_scene, model_viewer_mixin File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\crys3d\wx_model_viewer.py", line 10, in <module> from gltbx.wx_viewer import wxGLWindow File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\gltbx\wx_viewer.py", line 8, in <module> from gltbx.glu import * File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\gltbx\glu.py", line 3, in <module> ext = bp.import_ext("gltbx_glu_ext") File "C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\boost_adaptbx\boost\python.py", line 31, in import_ext raise ImportError( Dear All, I am getting this error when trying to run Phenix-refine. Any idea how to fix this? Thank you. Jobi ImportError: __import__("gltbx_glu_ext"): DLL load failed while importing gltbx_glu_ext: A dynamic link library (DLL) initialization routine failed. sys.path: C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\libsvm C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\phenix\wxGUI2\command_line C:\ProgramData\phenix-1.21.2-5419\python39.zip C:\ProgramData\phenix-1.21.2-5419\DLLs C:\ProgramData\phenix-1.21.2-5419\lib C:\ProgramData\phenix-1.21.2-5419 C:\ProgramData\phenix-1.21.2-5419\lib\site-packages C:\ProgramData\phenix-1.21.2-5419\lib\site-packages\mmtbx\suitename

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Error opening REEL and ligand refinement in Coot
by Marian Oliva 17 Jan '25

17 Jan '25

Dear all, I posted this problem a couple of days ago through phenix help mail address but I got no answer (not sure if it was delivered properly). Maybe here I am luckier. I have recently upgrade my machine to Ubuntu MATE 1.26 and re-install all crystallography software I often use, including Phenix version dev-5493. I am working in a structure of a protein bound to a new ligand. I built the ligand with chemDraw, get the SMILE, get a universal SMILE string in cactus.nci.nih.gov <http://cactus.nci.nih.gov/>, and used eLbow for ligand restraints generation and optimization (using default parameters). First problem. When I try to open the ligand in REEL. Phenix crash with the following message in the terminal libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so <http://nouveau_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: nouveau libGL error: MESA-LOADER: failed to open nouveau: /usr/lib/dri/nouveau_dri.so <http://nouveau_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: nouveau libGL error: MESA-LOADER: failed to open swrast: /usr/lib/dri/swrast_dri.so <http://swrast_dri.so/>: cannot open shared object file: No such file or directory (search paths /usr/lib/x86_64-linux-gnu/dri:\$${ORIGIN}/dri:/usr/lib/dri, suffix _dri) libGL error: failed to load driver: swrast The program 'main.py' received an X Window System error. This probably reflects a bug in the program. The error was 'BadValue'. (Details: serial 39668 error_code 2 request_code 152 minor_code 24) (Note to programmers: normally, X errors are reported asynchronously; that is, you will receive the error a while after causing it. To debug your program, run it with the --sync command line option to change this behavior. You can then get a meaningful backtrace from your debugger if you break on the gdk_x_error() function.) Second, when I open the structure in Coot (0.9.8.95) from Phenix and try to perform real space refine zone to the ligand, the attached window pops-up. Is this because I did something wrong during the installation? Is there a bug I am not aware of? Any help will be really appreciate. Many thanks in advance, Marian

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mmtbx.ringer with noise maps
by Schulz, Dr. Eike 15 Jan '25

15 Jan '25

Hi everyone, I am using mmtbx.ringer via phenix-1.21rc1-5127 to explore ED changes from END/RAPID maps. While it’s possible to provide volume scaled maps, it does seem possible to provide noise maps from END/RAPID is that correct or am I missing sth.? Related: setting gui=true enables to graphically browse through the results, it does not seem to be possible to automatically save all these plots. Is it possible to activate this? Best regards, Eike

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phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb
by fnsoxt＠qq.com 09 Jan '25

09 Jan '25

How can i deal with it? This is the log file Starting phenix.predict_and_build on Wed Jan 1 20:55:50 2025 by xukui =============================================================================== Processing files: ------------------------------------------------------------------------------- No files found Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- full_map=/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc seq_file=/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta resolution=4.1 nproc=20 predicted_model=/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb process_predicted_model.chunk_size=10000 predict_and_build.chunk_size=10000 process_predicted_model.break_into_chunks_if_length_is=10000 predict_and_build.break_into_chunks_if_length_is=10000 Warning: Ambiguous parameter definition: resolution = 4.1 Best matches: crystal_info.resolution prediction.resolution Assuming crystal_info.resolution was intended. Warning: Ambiguous parameter definition: nproc = 20 Best matches: prediction.nproc control.nproc Assuming control.nproc was intended. Processing files from PHIL: ------------------------------------------------------------------------------- Found model, /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb Found sequence, /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta Found real_map, /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { sequence_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" default_sequence = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" real_map_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" default_real_map = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" model { file = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" } default_model = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" } predict_and_build { break_into_chunks_if_length_is = 10000 chunk_size = 10000 } input_files { seq_file = /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta map_model { full_map = /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc } predicted_model = /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb } crystal_info { resolution = 4.1 } process_predicted_model { break_into_chunks_if_length_is = 10000 chunk_size = 10000 } control { nproc = 20 } Starting job =============================================================================== ************************************************************ PHENIX predict_and_build Wed Jan 1 20:55:59 2025 ************************************************************ Working directory: /data2/xukui/data/jobs_pab/6b3o PHENIX VERSION: 1.21.1-5286 Base directory is /data2/xukui/data/jobs_pab/6b3o Creating jobname of 'PredictAndBuild_0' Working directory /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn will be created in base directory Output prefix for files will be: /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_rebuilt Running in Standard mode... Turning off all building steps except refinement Running with a cryo-EM map Mean B-iso in af2_group_0.pdb: 80.9577007535 A**2 Added predicted model /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb_A with plddt=80.96 Mean value in B-factor field for /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb (converted from plddt to plddt): 80.96 Set random_seed_iterations to 5 No templates read from templates_as_string... Total of 0 templates to be used Setting density_modify_with_model = False (default for cryo-EM) Set rmsd_for_similar_placement to 4.10 A Working directory will be based on jobname: PredictAndBuild_0 Created new temp dir: PredictAndBuild_0 ... temp-dir will be deleted at end ================================================================================ Running predict_and_build ================================================================================ Starting data: Map file: Map manager (from /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc) Unit cell: (435.2, 435.2, 435.2, 90, 90, 90) Space group: P 1 (No. 1), Unit-cell grid: (320, 320, 320), (present: (320, 320, 320)), origin shift (0, 0, 0) Working coordinate shift (-0.0, -0.0, -0.0) NCS object with 0 groups: List of sequences: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK List of models: af2_group_0.pdb Chain A extracted List of chain IDs and sequences to use A (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK B (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK C (6b3o_A): MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK ================================================================================ Running cycle 1 of predict_and_build ================================================================================ Not using any supplied msas No supplied templates will be used in prediction this cycle ================================================================================ Predicting models for 0 chains with alphafold Updating chain names in model list... Chain A: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Total of 1 working models Total MSAs obtained: 0 Updating chain IDs Previous ID: 'A' New ID: 'A' MODEL: af2_group_0.pdb Getting processed (trimmed, B-values updated) models B-value field interpreted as pLDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Removing short segments: (chain A and resseq 537:539) Total of 492 of 605 residues kept after B-factor filtering Selection string for B-factor filtering: (chain A and resseq 15:20) or (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A and resseq 174:200) or (chain A and resseq 207:494) or (chain A and resseq 541:586) Selecting domains as compact chains Clusters: 15 Threshold: 3.90 Clusters: 5 Threshold: 4.40 Clusters: 6 Threshold: 4.82 Clusters: 5 Threshold: 4.34 Clusters: 3 Threshold: 3.27 Clusters: 2 Threshold: 2.14 Clusters: 3 Threshold: 3.98 Clusters: 2 Threshold: 1.81 Clusters: 3 Threshold: 3.74 Clusters: 2 Threshold: 1.80 Best resolution for domains is 35.0 A giving 3 regions Selection list based on domains: (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues) Total of 1 regions identified Obtained processed model from af2_group_0.pdb with 492 residues (of 605) =============================================================================== Finished with prediction (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) =============================================================================== =============================================================================== Getting scaffold model... (Job PredictAndBuild_0 cycle 1 at 2025-01-01 20:56:19) =============================================================================== Checking whether scaffold model is complete... ================================================================================ Getting new scaffold model in /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_scaffold_cycle_1.pdb ================================================================================ ================================================================================ Docking 1 models (to represent 3 sequences) in map to create a scaffold ================================================================================ Model to dock: af2_group_0.pdb: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Calculating how many copies of each sequence Model: A MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK Model copies: 1 Sequence copies: 3 Remainder copies: {'MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK': 0} remainder: 0 Copies to use: 3 Setting up model for dock_and_rebuild Added model af2_group_0.pdb (A) for dock_and_rebuild Running dock_and_rebuild to dock models Total of 1 predicted models MODEL: MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK ================================================================================ Running dock_and_rebuild on total of 3 chains Chain 1 (chain A from af2_group_0.pdb) Chain 2 (chain A from af2_group_0.pdb) Chain 3 (chain A from af2_group_0.pdb) ================================================================================ ================================================================================ Running on chain 1 (chain A from af2_group_0.pdb) ================================================================================ Working directory for this chain: PredictAndBuild_0/local_dock_and_rebuild_1_0 No docked model for chain A ... Running search... Running standard docking... =============================================================================== Processing input model =============================================================================== B-value field interpreted as pLDDT (0 - 100) Maximum rmsd of 1.50 A used Maximum B-value to be included: 59.22 A**2 Removing short segments: (chain A and resseq 537:539) Total of 492 of 605 residues kept after B-factor filtering Selection string for B-factor filtering: (chain A and resseq 15:20) or (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A and resseq 174:200) or (chain A and resseq 207:494) or (chain A and resseq 541:586) Selecting domains as compact chains Clusters: 15 Threshold: 3.90 Clusters: 5 Threshold: 4.40 Clusters: 6 Threshold: 4.82 Clusters: 5 Threshold: 4.34 Clusters: 3 Threshold: 3.27 Clusters: 2 Threshold: 2.14 Clusters: 3 Threshold: 3.98 Clusters: 2 Threshold: 1.81 Clusters: 3 Threshold: 3.74 Clusters: 2 Threshold: 1.80 Best resolution for domains is 35.0 A giving 3 regions Selection list based on domains: (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) or (resseq 207:494) or (resseq 541:586) (492 residues) Total of 1 regions identified Obtained processed model with 492 residues (of 605) Wrote processed model to /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0/local_dock_and_rebuild_1_0/working_model_processed.pdb =============================================================================== Extracting unique part of map =============================================================================== Setting map-model-manager and model shift to zero during run Split model into chains: A1 Chain number: 1 id: A1 Residues: 492 ============================================================================== Searching with each chain as a seed ============================================================================== ============================================================================== Running dock-in map on domain A1 with 492 residues ============================================================================== Running dock-in-map at overall resolution of 4.1 A Density radius set to: 24.6 A Placing model in map Map has been not been offset New cell after running map_box: (435.20, 424.32, 435.20, 90.00, 90.00, 90.00) Target boxes set to 20 Choosing local part of search model to use in search... Shifting search model coordinates (0.3, 1.9, -1.9) to origin and creating search map coefficients Docking with MR... Using masked map data MODEL: full_shifted_sm_1.pdb mass: 54120 (copies: 1) Estimated solvent fraction: 0.95 Total atoms in all copies: 3781 (volume = 66567.6 A**3) Solvent fraction (as used) is about 0.94 Total good sites: 11268 Max clusters: 1 Wrote mtz data to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/mtz_data.mtz Wrote model A1_full_shifted_sm_1.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A1_full_shifted_sm_1.pdb Wrote model A_from_cluster_0.pdb to PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A_from_cluster_0.pdb

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Re: phenix.predict_and_build, proccess normal and no error, but not generate the PredictAndBuild_0_overall_best.pdb
by Tom Terwilliger 09 Jan '25

09 Jan '25

On Thu, Jan 9, 2025 at 11:13 AM Oleg Sobolev <osobolev(a)lbl.gov> wrote: > Hi Tom, > > I fished out the following from my Spam folder, but it is on PhenixBB. Can > you please take a look? > > Best regards, > Oleg Sobolev. > > ---------- Forwarded message --------- > From: <fnsoxt(a)qq.com> > Date: Sun, Jan 5, 2025 at 8:03 PM > Subject: [phenixbb] phenix.predict_and_build, proccess normal and no > error, but not generate the PredictAndBuild_0_overall_best.pdb > To: <phenixbb(a)phenix-online.org> > > > How can i deal with it? This is the log file > > Starting phenix.predict_and_build > on Wed Jan 1 20:55:50 2025 by xukui > > =============================================================================== > > Processing files: > > ------------------------------------------------------------------------------- > > No files found > > Processing PHIL parameters: > > ------------------------------------------------------------------------------- > > Adding command-line PHIL: > ------------------------- > full_map=/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > seq_file=/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > resolution=4.1 > nproc=20 > > predicted_model=/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > process_predicted_model.chunk_size=10000 > predict_and_build.chunk_size=10000 > process_predicted_model.break_into_chunks_if_length_is=10000 > predict_and_build.break_into_chunks_if_length_is=10000 > > Warning: Ambiguous parameter definition: resolution = 4.1 > Best matches: > crystal_info.resolution > prediction.resolution > Assuming crystal_info.resolution was intended. > Warning: Ambiguous parameter definition: nproc = 20 > Best matches: > prediction.nproc > control.nproc > Assuming control.nproc was intended. > Processing files from PHIL: > > ------------------------------------------------------------------------------- > > Found model, /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > Found sequence, /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > Found real_map, /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > > Final processed PHIL parameters: > > ------------------------------------------------------------------------------- > data_manager { > sequence_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" > default_sequence = "/data2/xukui/data/jobs_pab/6b3o/6b3o.fasta" > real_map_files = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" > default_real_map = "/data2/xukui/data/jobs_pab/6b3o/6b3o.mrc" > model { > file = "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" > } > default_model = > "/data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb" > } > predict_and_build { > break_into_chunks_if_length_is = 10000 > chunk_size = 10000 > } > input_files { > seq_file = /data2/xukui/data/jobs_pab/6b3o/6b3o.fasta > map_model { > full_map = /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc > } > predicted_model = > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb > } > crystal_info { > resolution = 4.1 > } > process_predicted_model { > break_into_chunks_if_length_is = 10000 > chunk_size = 10000 > } > control { > nproc = 20 > } > > > Starting job > > =============================================================================== > > ************************************************************ > PHENIX predict_and_build Wed Jan 1 20:55:59 2025 > ************************************************************ > > Working directory: /data2/xukui/data/jobs_pab/6b3o > > PHENIX VERSION: 1.21.1-5286 > > Base directory is /data2/xukui/data/jobs_pab/6b3o > Creating jobname of 'PredictAndBuild_0' > Working directory > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn will be created > in base directory > Output prefix for files will be: > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_rebuilt > Running in Standard mode... > Turning off all building steps except refinement > > Running with a cryo-EM map > Mean B-iso in af2_group_0.pdb: 80.9577007535 A**2 > Added predicted model > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb_A with > plddt=80.96 > Mean value in B-factor field for > /data2/xukui/data/jobs_pab/6b3o/templ_af2/af2_group_0.pdb (converted from > plddt to plddt): 80.96 > Set random_seed_iterations to 5 > No templates read from templates_as_string... > Total of 0 templates to be used > Setting density_modify_with_model = False (default for cryo-EM) > > Set rmsd_for_similar_placement to 4.10 A > Working directory will be based on jobname: PredictAndBuild_0 > Created new temp dir: PredictAndBuild_0 ... > temp-dir will be deleted at end > > > ================================================================================ > Running predict_and_build > > ================================================================================ > > Starting data: > Map file: Map manager (from /data2/xukui/data/jobs_pab/6b3o/6b3o.mrc) > Unit cell: (435.2, 435.2, 435.2, 90, 90, 90) Space group: P 1 (No. 1), > Unit-cell grid: (320, 320, 320), (present: (320, 320, 320)), origin shift > (0, 0, 0) > Working coordinate shift (-0.0, -0.0, -0.0) > NCS object with 0 groups: > > List of sequences: > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > List of models: > af2_group_0.pdb Chain A extracted > > List of chain IDs and sequences to use > A (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > B (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > C (6b3o_A): > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > > ================================================================================ > Running cycle 1 of predict_and_build > > ================================================================================ > Not using any supplied msas > No supplied templates will be used in prediction this cycle > > > ================================================================================ > Predicting models for 0 chains with alphafold > > Updating chain names in model list... > Chain A: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Total of 1 working models > Total MSAs obtained: 0 > > Updating chain IDs > Previous ID: 'A' New ID: 'A' > MODEL: af2_group_0.pdb > > Getting processed (trimmed, B-values updated) models > B-value field interpreted as pLDDT (0 - 100) > Maximum rmsd of 1.50 A used > Maximum B-value to be included: 59.22 A**2 > Removing short segments: (chain A and resseq 537:539) > Total of 492 of 605 residues kept after B-factor filtering > > Selection string for B-factor filtering: (chain A and resseq 15:20) or > (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A > and resseq 174:200) or (chain A and resseq 207:494) or (chain A and > resseq 541:586) > > Selecting domains as compact chains > Clusters: 15 Threshold: 3.90 > Clusters: 5 Threshold: 4.40 > Clusters: 6 Threshold: 4.82 > Clusters: 5 Threshold: 4.34 > Clusters: 3 Threshold: 3.27 > Clusters: 2 Threshold: 2.14 > Clusters: 3 Threshold: 3.98 > Clusters: 2 Threshold: 1.81 > Clusters: 3 Threshold: 3.74 > Clusters: 2 Threshold: 1.80 > Best resolution for domains is 35.0 A giving 3 regions > > Selection list based on domains: > (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) > or (resseq 207:494) or (resseq 541:586) (492 residues) > Total of 1 regions identified > Obtained processed model from af2_group_0.pdb with 492 residues (of 605) > =============================================================================== > > Finished with prediction (Job PredictAndBuild_0 cycle 1 at 2025-01-01 > 20:56:19) > =============================================================================== > > > =============================================================================== > > Getting scaffold model... (Job PredictAndBuild_0 cycle 1 at 2025-01-01 > 20:56:19) > =============================================================================== > > > > Checking whether scaffold model is complete... > > > > ================================================================================ > Getting new scaffold model in > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0_CarryOn/PredictAndBuild_0_scaffold_cycle_1.pdb > > ================================================================================ > > > ================================================================================ > Docking 1 models (to represent 3 sequences) in map to create a scaffold > > > ================================================================================ > Model to dock: af2_group_0.pdb: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Calculating how many copies of each sequence > Model: A > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > Model copies: 1 Sequence copies: 3 > Remainder copies: > {'MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK': > 0} remainder: 0 > Copies to use: 3 > Setting up model for dock_and_rebuild > Added model af2_group_0.pdb (A) for dock_and_rebuild > > Running dock_and_rebuild to dock models > > Total of 1 predicted models > MODEL: > MKLCILLAVVAFVGLSLGRSLASVSTGYRLTTFEPYTPMLVNDSVQSVDGLYEMQIPTNFTIGHHEEFIQTRSPKVTIDCAAFVCGDNTACRQQLVEYGSFCVNVNAILNEVNNLLDNMQLQVASALMQGVTISSRLPDGISGPIDDINFSPLLGCIGSTCAEDGNGPSAIRGRSAIEDLLFDKVKLSDVGFVEAYNNCTGGQEVRDLLCVQSFNGIKVLPPVLSESQISGYTTGATAAAMFPPWSAAAGVPFSLSVQYRINGLGVTMNVLSENQKMIASAFNNALGAIQDGFDATNSALGKIQSVVNANAEALNNLLNQLSNRFGAISASLQEILTRLEAVEAKAQIDRLINGRLTALNAYISKQLSDSTLIKVSAAQAIEKVNECVKSQTTRINFCGNGNHILSLVQNAPYGLYFIHFSYVPISFTTANVSPGLCISGDRGLAPKAGYFVQDDGEWKFTGSSYYYPEPITDKNSVIMSSCAVNYTKAPEVFLNTSIPNPPDFKEELDKWFKNQTSIAPDLSLDFEKLNVTLLDLTYEMNRIQDAIKKLNESYINLIKRMKQIEDKIEEIESKQKKIENEIARIKKIKLVPRGSLEWSHPQFEK > > > ================================================================================ > Running dock_and_rebuild on total of 3 chains > Chain 1 (chain A from af2_group_0.pdb) > Chain 2 (chain A from af2_group_0.pdb) > Chain 3 (chain A from af2_group_0.pdb) > > ================================================================================ > > > ================================================================================ > Running on chain 1 (chain A from af2_group_0.pdb) > > ================================================================================ > Working directory for this chain: > PredictAndBuild_0/local_dock_and_rebuild_1_0 > No docked model for chain A ... > Running search... > > Running standard docking... > > =============================================================================== > > Processing input model > =============================================================================== > > > B-value field interpreted as pLDDT (0 - 100) > Maximum rmsd of 1.50 A used > Maximum B-value to be included: 59.22 A**2 > Removing short segments: (chain A and resseq 537:539) > Total of 492 of 605 residues kept after B-factor filtering > > Selection string for B-factor filtering: (chain A and resseq 15:20) or > (chain A and resseq 25:136) or (chain A and resseq 145:157) or (chain A > and resseq 174:200) or (chain A and resseq 207:494) or (chain A and > resseq 541:586) > > Selecting domains as compact chains > Clusters: 15 Threshold: 3.90 > Clusters: 5 Threshold: 4.40 > Clusters: 6 Threshold: 4.82 > Clusters: 5 Threshold: 4.34 > Clusters: 3 Threshold: 3.27 > Clusters: 2 Threshold: 2.14 > Clusters: 3 Threshold: 3.98 > Clusters: 2 Threshold: 1.81 > Clusters: 3 Threshold: 3.74 > Clusters: 2 Threshold: 1.80 > Best resolution for domains is 35.0 A giving 3 regions > > Selection list based on domains: > (resseq 15:20) or (resseq 25:136) or (resseq 145:157) or (resseq 174:200) > or (resseq 207:494) or (resseq 541:586) (492 residues) > Total of 1 regions identified > Obtained processed model with 492 residues (of 605) > Wrote processed model to > /data2/xukui/data/jobs_pab/6b3o/PredictAndBuild_0/local_dock_and_rebuild_1_0/working_model_processed.pdb > > =============================================================================== > > Extracting unique part of map > =============================================================================== > > > > Setting map-model-manager and model shift to zero during run > Split model into chains: A1 > Chain number: 1 id: A1 Residues: 492 > > ============================================================================== > > Searching with each chain as a seed > ============================================================================== > > > > ============================================================================== > > Running dock-in map on domain A1 with 492 residues > ============================================================================== > > > > Running dock-in-map at overall resolution of 4.1 A > Density radius set to: 24.6 A > Placing model in map > > Map has been not been offset > New cell after running map_box: (435.20, 424.32, 435.20, 90.00, 90.00, > 90.00) > Target boxes set to 20 > > Choosing local part of search model to use in search... > > Shifting search model coordinates (0.3, 1.9, -1.9) to origin > and creating search map coefficients > > Docking with MR... > Using masked map data > MODEL: full_shifted_sm_1.pdb mass: 54120 (copies: 1) > Estimated solvent fraction: 0.95 > Total atoms in all copies: 3781 (volume = 66567.6 A**3) > Solvent fraction (as used) is about 0.94 > Total good sites: 11268 > Max clusters: 1 > Wrote mtz data to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/mtz_data.mtz > Wrote model A1_full_shifted_sm_1.pdb to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A1_full_shifted_sm_1.pdb > Wrote model A_from_cluster_0.pdb to > PredictAndBuild_0/local_dock_and_rebuild_1_0/run_mr/A_from_cluster_0.pdb > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s > -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Error phenix refine with ligands
by miriam.cavinato＠unimi.it 07 Jan '25

07 Jan '25

Hi everyone, I am trying to refine my model containing a ligand (a thiophene -like molecule with a 7 carbon atom cycle attached). I create restraints with ready set utility or directly with eLBOW, then I use phenix.refine and I get this error: "fatal problems in interpreting model file: number of atoms with unknown nonbonded energy type symbols: 12 Please edit the model file to resolve the problems or/and supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definition if necessary". Another problem is that as soon as I try to open REEL or open any result to check restraints, Phenix crashes... I was wondering if someone has the same issue and can help me figure it out! Thanks in advance Best regards Miriam

3 2