- phenixbb - phenix-online.org

map-to-model FSC on low resolution map
by bluufive2＠gmail.com 26 May '25

26 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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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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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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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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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 04 Apr '25

04 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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