- phenixbb - phenix-online.org

Submission deadline on Monday
by Nick DeHaan 06 Dec '19

06 Dec '19

Hi PhenixBB, The extended deadline for the AIMS Awards program is less than a week away! If any PIs, postdocs, or grad students you know are interested in submitting a proposal, please remind them to apply on the website by Monday, December 9th. Website: www.atomwise.com/aims <http://bit.ly/2PkkOlB> Best regards, Nick Nick DeHaan *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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15 PhD scholarships in Braunschweig, Germany
by Blankenfeldt, Wulf 29 Nov '19

29 Nov '19

Dear colleagues & prospective Ph.D. students, The Technische Universität Braunschweig in collaboration with Helmholtz Centre for Infection Research and Ostfalia University of Applied Sciences currently initiate the doctoral program "Drug Discovery and Cheminformatics for New Anti-Infectives (iCA)" which is granted by the Ministry of Science and Culture of Lower Saxony. The program aims at studying fundamental principles of drug discovery by combining life sciences and digital sciences. The iCA consortium is offering 15 Georg-Christoph-Lichtenberg scholarships (duration: 3 years). The program of the iCA consortium offers an ambitious, structured and interdisciplinary training based on top-level fundamental research. This joint program provides an internationally competitive research environment with state-of-the-art facilities. The participating groups use a variety of different methods, including experimental, digital, and theoretical approaches. More information about specific projects and participating groups can be found at: https://www.tu-braunschweig.de/en/pharmchem/translate-to-english-promotions… The graduate program starts in the period from February to July 2020. For details and individual project descriptions please refer to the scholarship announcement attached. If you have any questions, please contact pvz-apply(a)tu-braunschweig.de<mailto:[email protected]>. The program is open for applications now. Applications should include letter of motivation, curriculum vitae, certificates, etc. combined in a single PDF file (max. 15 MB). Please send your application to pvz-apply(a)tu-braunschweig.de<mailto:[email protected]> until 31 December, 2019. Please forward these information to interested colleagues. Kind regards, Wulf Blankenfeldt ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Position at Diamond: XChem Beamline Scientist
by Frank Von Delft 29 Nov '19

29 Nov '19

Dear all, We are recruiting as permanent position a Beamline Scientist on the XChem fragment screening facility at Diamond. This role is to join the XChem team to support academic and industrial users with experiments and service work, co-manage the XChem lab, develop new fragment-related methodologies, and over next few years, work on expanding the XChem offering beyond hit identification. If you are a technically-minded crystallographer that enjoys teaching or training people, like an organised life, thrive on collaboration and like to see how you're making others productive, you will enjoy this job. Besides, Diamond is incredibly collegial and has a terrific user community. The ad is here: https://vacancies.diamond.ac.uk/vacancy/xchem-beamline-scientist-404499.html (for some reason you may need to click twice on the link to make it work). The application deadline is the 15th Dec 2019, and we wil linterview on 17th Dec (i.e. before Xmas). If you have questions, contact me or Alice Douangamath <Alice.Douangamath(a)diamond.ac.uk><mailto:[email protected]>, who heads the facility. Frank -- Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile) Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F)

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Re: [phenixbb] Real space refine of long side chains
by Leonid Sazanov 27 Nov '19

27 Nov '19

Hi, We have addressed exactly this problem by writing a script, in which B-factors are refined first and only then real-space refinement happens. This allows disordered side-chains to acquire high B-factors and so they are not pulled into backbone anymore. This cycle is repeated twice to achieve convergence. Parameters for B-factor refinement (ADP restrains) were optimized to account for consistent lack of density for acidic side chains in cryoEM. It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636 If needed, I can send a script. Best Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at Date: Mon, 25 Nov 2019 19:11:16 +0000 From: Luca Pellegrini <lp212(a)cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Real space refine of long side chains Message-ID: <37F0D7B2-3C9E-4FE1-B0BF-6B23F0D8925B(a)cam.ac.uk> Content-Type: text/plain; charset=us-ascii I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards... Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Group ADP refinement restraints
by Taylor Stevens 27 Nov '19

27 Nov '19

Hello, I am currently refining a low-ish resolution structure (through the phenix.refine GUI) with phenix version 1.14 and had some questions about the use of restraints in group ADP refinement. In the phenix.refine documentation (https://www.phenix-online.org/documentation/reference/refinement.html#refin… <https://www.phenix-online.org/documentation/reference/refinement.html#refin…>) it is stated that “Group isotropic ADP or TLS refinement do not use any restraints”, however, this does not seem to be the case. If I look in the log file I can see the following lines of text which I believe indicate that the restraints are being applied: |-group b-factor refinement (macro cycle = 0; iterations = 0)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = None | |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 1; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 2; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 3; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| If I manually set the wu parameter to 0 under “Refinement target weights" nothing changes, however, if I navigate to "All parameters > ADP settings > Group B-Factors" in the GUI there is a “Use restraints” box that is checked by default. If I uncheck this box, there are no longer any restraints being applied according to the log file, and in the case of the structure I am refining, there is a substantial drop in the rfree/rwork. Is this an issue with the program or documentation? Or am I misunderstanding how the program is supposed to work? Is it generally a good idea to use group ADP refinement without restraints? Thanks, Taylor

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Real space refine of long side chains
by Luca Pellegrini 26 Nov '19

26 Nov '19

I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards... Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Software developer role at Diamond Light Source
by Hall, Dave (DLSLtd,RAL,LSCI) 25 Nov '19

25 Nov '19

Dear all We currently have a role for a software developer to work with the MX group at Diamond Light Source (www.diamond.ac.uk/mx<http://www.diamond.ac.uk/mx>). The successful candidate will work with scientific staff and software developers to enable experiments across the diverse suite of MX beamlines. For details of the role and how to apply see here https://vacancies.diamond.ac.uk/vacancy/data-acquisition-scientist-for-stru… Best regards Dave Hall MX Group Diamond Light Source -- This e-mail 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 authorised 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 the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail 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. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Postdoc position in methods development at LBNL
by Dorothee Liebschner 23 Nov '19

23 Nov '19

Announcing a postdoc position on behalf of Dr. Kanupriya Pande: ======================================================================== Post-doc position in methods development in the Molecular Biophysics and Integrated Bioimaging division at LBL. The overall objectives of the project are to develop theory and computation to extract conformational heterogeneity and disorder from diffraction and imaging data. The position is available immediately with an initial appointment for 2 years with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Qualified candidates must have a PhD in Biophysics, Physics, Mathematics, Chemistry, or related fields. Job description and how to apply: https://lbl.referrals.selectminds.com/jobs/computational-biologist-postdoc-… ======================================================================== -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [phenixbb] weight optimization in refinement
by Alexei Gorelik 23 Nov '19

23 Nov '19

Thanks! What I meant is, phenix.refine seems to run a number of optimization threads (usually 10-14) independent of the number of cores specified (for example, 4 or 8). If i specify 8 cores, is there a way to force it to run 8 weight optimizations? On Nov 22, 2019 1:24 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: Hi Alexei, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? nproc parameter controls number of CPUs to be used in weight optimization. Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? No. There is some built-in logic, phenix.refine does it when these conditions are met and it can un-do the result if it is not an improvement. Is there particular need to do this in your context? Pavel

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problems running refinement of shaken model against half map
by L. Hielkema 23 Nov '19

23 Nov '19

Hi all, For the validation of my model to my map in phenix 1.17.1 I tried to refine my shaken model (0.5Å) against my half map in phenix real space refine. However, whatever I try I get a weird behaviour in the FSC(Model-map), see the image below. It seems not to be able to reach 0 in the correlation, but keeps getting stuck at 0.1. I tried various things to solve this, but unfortunately nothing helps: - Using the other half map - Cut of the heterogeneous part of my model and map and refine this - Used refined data without using a mask for the last iterations - Used different resolutions to refine against - Tried data from someone else in the lab (same microscope, same imaging conditions), to check if I am doing something wrong (this gave good results) When doing the same refinement in Refmac5 in ccpem 1.4 it does seem to work, however I would not like to switch programs, because this will mess up my final model. Best, Lisa

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weight optimization in refinement
by Alexei Gorelik 23 Nov '19

23 Nov '19

Hi, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? Most of the time, when the "real-space" option is selected, it only carries out rotamer fitting (rsrl). I do know there's a separate real-space refinement program in Phenix. Thanks!

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Secondary structure restraints
by Luca Pellegrini 21 Nov '19

21 Nov '19

I have a protein-DNA complex and would like to apply SS restraints. What is the best way to apply the SS restraints to the protein only, using the GUI? I have tried the following: Select ‘Use secondary structure restraints’ in the ‘Refinement Settings’ tab ‘Select Atoms’ In the Selection Editor window, 'Find Secondary Structures' Removed manually all nucleic acid restraints in ‘Base Pairs’ and Stacking Pairs’ tabs Save and close. However, phenix refinement keeps switching SS restraints for nucleic acids to True. Kind regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Molybdenum cofactor refinement
by Cristiano Mota 21 Nov '19

21 Nov '19

Hi all, I'm using phenix.refine to refine a structure of a Molybo-protein at 1.9Å. The MGD cofactors (molybdopterin guanine dinucleotide) are being refined with a weird distorted geometry causing some clashes. The Fo-Fc maps show that something is going wrong in the aromatic rings interatomic distances. I'm using the readyset to pick up MGD and metal restraints. Am I using the right protocol? Best regards, Cristiano Mota -- *Cristiano de Sousa Mota* Postdoctoral Researcher, Macromolecular Crystallography Group UCIBIO / FCT - Universidade Nova de Lisboa 2829-516 Caparica, Portugal (00351 212948300, ext 10962) http://xtal.dq.fct.unl.pt/

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Deadline Extended to December 9th
by Nick DeHaan 21 Nov '19

21 Nov '19

Hi PhenixBB, Thanks for sharing information about the AIMS Awards with your colleagues! Many have told us they really appreciated it. We’ve had requests for more time - so we extended the deadline to December 9th! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development efforts, and get published. The program is open to investigators, postdocs, and graduate students worldwide. We encourage you to check out our flyer for more information: Flyer <http://bit.ly/37oIrS3> You can apply directly on the website: atomwise.com/aims. Please don't hesitate to reach out with any questions! Best, Nick Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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cryo-EM density modification
by Tom Terwilliger 19 Nov '19

19 Nov '19

Hi Phenix cryo-EM users, For those of you trying out density modification for cryo-EM (phenix.resolve_cryo_em), the automatic estimation of resolution in the current version uses unmasked resolution instead of masked, in some cases resulting in running density modification at too low a resolution. Consequently it is best with this version if you specify your nominal resolution. To run it you can type: phenix.resolve_cryo_em half_map_1.ccp4 half_map_2.ccp4 \ seq_file=seq.dat resolution=3.5 or something like that. It requires the current nightly build to run. You might also want to wait just a short while and a version that has this and a few other bugs fixed, a GUI, full documentation, and an example dataset will be out (hopefully this week). The full description of the method is at https://www.biorxiv.org/content/10.1101/845032v1 Let me know of any problems or suggestions! All the best, Tom T -- 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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Differences in refinement statistics
by Chancievan Thangaratnarajah 19 Nov '19

19 Nov '19

Hello, I have noticed differences in the refinement statistics between two different Phenix versions (see attachments) even though I am using the same cryo-EM map and model as input. The most notable difference are rotamer outliers, which were 0 % in Phenix 1.16-3549 and now 6 % in Phenix 1.17-3660. I was wondering whether anyone has noticed a similar behaviour? Or is there something that I have missed? Best, Chancie.

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Error in sequence assignment
by Tom Terwilliger 18 Nov '19

18 Nov '19

Hi Nicholas, I'm afraid there isn't a way to say which sequence goes with which chain. I would suggest using the tool phenix.replace_side_chains. Give it 1 chain and 1 sequence and if they have the same length it should just put it in. If it doesn't work, try phenix.sequence_from_map which can do the same thing. Let me know if that doesn't do it! All the best, Tom T Date: Sun, 17 Nov 2019 17:07:16 -0500 From: Nicholas Gao <dominion146(a)GMAIL.COM> Subject: Specify chain assignment in sequence file for rebuild-in-place of phenix.autobuild Dear CCP4, I currently have an MR solution that has the wrong sequence. The pdb file of the solution contains 3 chains, and I'd like to use the rebuild-in-place functionality within phenix.autobuild to correct the sequence of all 3 chains. Phenix allows me to supply a sequence file as input for this job, it's not clear to me how I tell the program which sequence should be assigned to which chain. Anyone know how to do this? Sincerely, Nicholas Gao -- 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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RapiData at SSRL 2020 - application deadline extended by one week!
by Smith, Clyde 16 Nov '19

16 Nov '19

Hi all, We have extended the deadline for applications for a place at the RapiData 2020 @ SSRL workshop to next Friday, November 22 2019! There are still a few spots left, so get your application in! The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu csmith(a)slac.stanford.edu jwierman(a)slac.stanford.edu

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General interest
by John R Helliwell 15 Nov '19

15 Nov '19

Dear Colleagues, I imagine the two articles that I describe in my posting at the IUCr’s Forum will be of interest to the MX community. See:- https://forums.iucr.org/viewtopic.php?f=39&t=427 All best wishes, John Emeritus Professor John R Helliwell DSc

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Scientist job position at AbbVie
by Longenecker, Kenton L 14 Nov '19

14 Nov '19

Hi - I'd like to draw attention of interested candidates to the following job opportunity with full description to apply at: http://abbvie.referrals.selectminds.com/jobs/senior-scientist-i-ii-protein-… Company overview: AbbVie (NYSE:ABBV) is a global, research-driven biopharmaceutical company committed to developing innovative advanced therapies for some of the world's most complex and critical conditions. The company's mission is to use its expertise, dedicated people and unique approach to innovation to markedly improve treatments across four primary therapeutic areas: immunology, oncology, virology and neuroscience. In more than 75 countries, AbbVie employees are working every day to advance health solutions for people around the world. Job Description: The Structural Biology Group at AbbVie Headquarters in Lake County, Illinois, USA is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern structural biology techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Senior Scientist will utilize X-ray crystallography techniques to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. ________________________________ Kenton Longenecker, Ph.D. Sr. Principal Research Scientist AbbVie R&D Discovery, DDST Structural Biology 1 N. Waukegan Road, AP10-LL North Chicago, IL 60064 OFFICE 847-938-1428 EMAIL kenton.longenecker(a)abbvie.com<mailto:%[email protected]> abbvie.com<http://www.abbvie.com> This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. ________________________________

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Submissions to the Computational Crystallography Newsletter – 30 NOV 19
by Nigel Moriarty 12 Nov '19

12 Nov '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2020 issue is 30 November 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Postdoc Position in Berkeley
by Petrus Zwart 09 Nov '19

09 Nov '19

Dear All, We have two postdoc positions open in LBNL's Center for Advanced Mathematics in Energy Research Applications (CAMERA; https://www.camera.lbl.gov/) to work on a diverse set of problems in managing, cleaning and interpreting biophysical data ranging from microscopy to crystallography. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88805 https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Feel free to contact me for more information. Regards Peter Zwart -- ------------------------------------------------------------------------ P.H. Zwart Staff Scientist Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -------------------------------------------------------------------------

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RapiData at SSRL 2020 reminder - just over a week left to apply!
by Smith, Clyde 05 Nov '19

05 Nov '19

Hi all, A reminder that there is only a week left to apply for a place at the RapiData 2020 @ SSRL workshop. Applications close the middle of this month, November 15 2019. The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu jwierman(a)slac.stanford.edu csmith(a)slac.stanford.edu

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Phenix version 1.17 released
by Paul Adams 04 Nov '19

04 Nov '19

The Phenix developers are pleased to announce that version 1.17 of Phenix is now available (build 1.17.1-3660). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that there is a new publication that describes recent Phenix developments for structure determination with X-rays, neutrons and electrons: https://doi.org/10.1107/S2059798319011471 Highlights for the 1.17 version of Phenix: 1.17.1 Changes - Fix bug on Windows where xtriage results would fail to display - Other bug fixes 1.17 Changes - Improved handling of SHELX data in phenix.reflection_file_converter - eLBOW can output files for Amber and supports the Orca QM package - dials.image_viewer is used for viewing diffraction images - Updated map smoothing - Fix inconsistency in clashscore values in phenix.validation_cryoem when hydrogens are in the model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Nikki Humphreys [ nhumphreys(a)lbl.gov ][ 1-510-486-4610 ] --

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Postdoc position available in LBNL
by Peter Zwart 01 Nov '19

01 Nov '19

Dear All, We have a postdoc position available at LBNL to work on the development of computational approaches for twinned crystallographic data. This is an exciting opportunity to address a relatively common phenomenon in crystallographic data analysis for which there are currently limited twinning-aware approaches. The aim is to develop tools that impact substructure solution, molecular replacement, density modification and structure refinement. Click the link below for more info or contact me directly. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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Understanding Biology through Structure 16-20 March 2020
by Tom Terwilliger 31 Oct '19

31 Oct '19

Hi Colleagues, particularly students and postdocs, I would like to encourage you to sign up for "Understanding Biology through Structure 2020" (https://cvent.me/4kq9P, March 16-20, 2020 in Santa Fe,NM). Student and postdoc fellowships covering registration and hotel are available (awarded competitively after registration on a rolling basis). The conference is a forum where students and postdocs can meet established researchers and discuss the latest methods and results. For a one-line review and info on the last one see https://bit.ly/2Gfkm4t and https://bit.ly/2Gg39rm. Confirmed speakers are Ilme Schlichting, Yvonne Jones, Hao Wu, Peijun Zhang, Christopher Russo, Claudio Ciferri, David Stuart, Blake Wiedenheft, Ci Ji Lim, Robert Stroud, Wayne Hendrickson, Bonnie Murphy, Anne Houdusse-Juille, Sonja Lonrenz, Chris Hill, Chun-wa Chung, Jian Payandeh, Amit Sharma, Marissa Matsumoto, Suzanne Scarlata, Osamu Nureki, Natalia Jura, Erica Ollmann Saphire, Eva Nogales, Andrej Sali, Anke Bill, Joanna Sulkowska, David Eisenberg, Marie Pancera, Karla Satchell, Jacques Philippe Colletier, Tom Terwilliger, Christopher Neale, and Tom Blundell. All the talks will be followed by 10-15 minutes of discussion with participation by students and postdocs especially encouraged. After the main conference there will be an optional Phenix workshop with lectures and hands-on sessions on using Phenix for crystallography and cryo-EM. Registration is first-come first served, with a limit of 120. All the best, Tom T -- 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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GUI reorders file data type in EM validation task
by Ashley Pike 31 Oct '19

31 Oct '19

Hi, I am having problems convincing the GUI which EM map is which for halfmap validation. Version is 1.17-3644 Here is input: [cid:[email protected]] and what is written to Summary tab: [cid:[email protected]] Any tricks to getting this to work? Editing the .eff file written by the gui is an option but running phenix.validation_cryoem on the command line doesn't seem to produce much viewable output. Cheers, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford Phone: +44 (0)1865 617576 | FAX: +44 (0)1865 617575 | ashley.pike(a)sgc.ox.ac.uk<mailto:[email protected]> | www.thesgc.org<http://www.thesgc.org/> Address: Structural Genomics Consortium, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK

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Potential Berkeley Server Outage (October 25)
by Billy Poon 30 Oct '19

30 Oct '19

Hi everyone, As a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will probably be shut down today and will return next week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Berkeley Server Outage (Starting October 26th)
by Paul Adams 26 Oct '19

26 Oct '19

Dear Colleagues, yet again, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down this weekend and will return later the following week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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real space refine and nonbonded_weight
by Cheung, Alan 26 Oct '19

26 Oct '19

Dear Developers A structure we refined back in 2017, using phenix.real_space_refine on a cryoEM map @ 3.7A (version 1.11.1–2575) produces a clashscore of ~8 but the exact same refinement run with the latest phenix (version 1.17.1) generates a clashscore of ~22. Our refinements with the latest version on other EM structures tend to generate pretty high clashscores too. I think i've tracked this down to the nonbonded_weight parameter, which defaults to 1000 in the older version, and to 100 in the latest version. At which version did the default change, and is there a reason for it? I couldn't find it in the changelog. Alan

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rosetta.run_tests crash
by wtempel 25 Oct '19

25 Oct '19

Hi, has anyone tried the combination of phenix-1.17 and rosetta-2019.40? Crashes in my hands, crash log attached. I may have modified the phenix installation by phenix.python -m pip install readline, in case it matters. Any suggestions appreciated. Many thanks in advance. Wolfram Tempel

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Yeast microtubule model
by Sebastiano Pasqualato 24 Oct '19

24 Oct '19

Dear all, I’m addressing to people working in the microtubule field. Has someone created, or knows where I could find, a pdb file of the yeast microtubule, or a portion of it? I’m interested in studying the contacts between subunits within the lattice. I know one could generate that using yeast tubulin dimers, but I don’t know exactly how. If someone has already done that and is willing to share it, that would be extremely helpful. Thanks a lot in advance, ciao, S PS: sorry for the cross posting to members of both bulletin boards. -- Sebastiano Pasqualato, PhD Biochemistry and Structural Biology Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

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Phenix-RSR model fit issue in CS-Map
by pramod kumar 24 Oct '19

24 Oct '19

Dear Experts, I have a map generated through cryosparc (ab initio-reconstr and homo-refine at 3.7A* FSC and sharpened in Scipion and separately in EMAN2). I have build the initial pdb through BALBES which has perfect validation parameters and nice fitting in the map (with the mtz output) but the co-ordinates are shifted from the true origin of CS-map. I used phenix-RSR to fit and refine, but validation results remained too far to accept the model as good solution and also a small region entered in wrong nearyby densities. So far following independent and downstream approaches I have taken:- In phenix; dock in map, map to model, rigid body refine followed by real space refine (with both .map and converted .mtz), using only chain A-map boxing and model generation through NCS. I have tried chimera fit for entire assembly and also only one chain in boxed map and full map but still the validation remained far from acceptable values and a small region in wrong neighboring density. Please help. -- Best regards, Promod

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errors in rosetta.refine
by Bram mylemans 18 Oct '19

18 Oct '19

dear I am trying to run rosetta.refine but get an error. I am using the latest version of phenix (1.17-3644) and I have tried to versions of rosetta (3.10 release date 2 Oct 2018 and 3.11 release date 26 Sept 2019) If I run rosetta.run_tests with rosetta 3.10 I get the following error message: DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: Segmentation fault (core dumped) If I run with rosetta 3.11 I get a different error message: DEBUG dumping error message ERROR: Rosetta exited with status 127 stderr output: /opt/rosetta_3.11_phenix/main/source/bin/rosetta_scripts.python.linuxgccrelease: error while loading shared libraries: libcifparse.so: cannot open shared object file: No such file or directory Are these version of rosetta and phenix compatible?

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Small Molecule Discovery RFP - Deadline is October 28th
by Nick DeHaan 18 Oct '19

18 Oct '19

Hi PhenixBB, I thought this group might be interested in an academic research support program that helps identify new active compounds based on protein structure. The award provides investigators, postdocs, or grad students with approximately 72 small molecules predicted by machine learning to bind to their protein of interest. A few awards also provide in-kind support (with a value of up to $20k) for the assay work. Applications take ~30 minutes to complete, and >300 awards will be given out this cycle. Proposals are due by October 28th. You can find out more here: Website: www.atomwise.com/aims <http://bit.ly/31rz1B4> Infographic: http://www.atomwise.com/wp-content/uploads/2019/10/AIMS-Infographic-Stats_F… <http://bit.ly/31jRa3O> Flyer: http://www.atomwise.com/wp-content/uploads/2019/10/Atomwise-AIMS-Awards-Fly… <http://bit.ly/31nkVAI> Please feel free to reach out to me with any questions! Best regards, Nick Nick DeHaan, MsE *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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Job opening: Scientist-I (Structural Biology) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 18 Oct '19

18 Oct '19

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology. The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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high B Factor after real space refinement against a cryoEM map
by Keda Zhou 17 Oct '19

17 Oct '19

Dear all, I am trying to do the real space refinement for my model against a 5.0 angstrom cryoEM map. All parameters look pretty good except the B factor. The mean of the B factor is close to 400. I am just wondering whether the low resolution makes the B factor this high. Does anyone have any idea or suggestion on the high B factor during real space refinement? Is it possible to reduce it? What is the actual meaning of this B factor? Thanks in advance. cody

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Two tenure-track faculty openings at Univ. of Missouri Biochemistry
by Tanner, John J. 15 Oct '19

15 Oct '19

Dear Colleagues, My department has two tenure-track faculty openings. Review of applications will begin on November 15, 2019. Click the link below for more information. https://biochem.missouri.edu/open-positions/ John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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file location changed
by Cygler, Miroslaw 14 Oct '19

14 Oct '19

Hi, In order to allow synchronization of files on my mac with the cloud server I had to move all files used by Phenix to a new directory, including the main Phenix folder. How do I change the paths to these files in phenix so that they are accessible to the software? Phenix would not start without the main Phenix folder returned back to the old location. How do I rectify this as well? Thanks for your help, Mirek

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advert for PostDoc position @Singapore
by SR Bharath 14 Oct '19

14 Oct '19

Dear Colleagues, We are seeking an enthusiastic and self-motivated postdoctoral research fellow to study proteins involved in maintaining genome stability and the Hippo signaling pathway. We take a combinatorial approach of molecular biology, biochemical and biophysical methods, and structural biology (macromolecular crystallography and electron cryomicroscopy). Significant aspects of our projects have translational potential. The candidate is expected to be involved in the development of small molecules/peptides for cancer therapeutics. Singapore is an excellent environment to do research with many research groups close by in Biopolis [https://www.a-star.edu.sg/imcb]. A*STAR offers highly competitive salaries with benefits including housing allowance and 1-3 months performance bonus. Requirements: · PhD in biochemistry, biophysics, molecular & cell biology or in medicinal chemistry · Practical experiences in structural biology (Electron Cryomicroscopy and/or X-ray crystallography) or in medicinal chemistry · Good publication record · Competent in scientific writing Interested applicants should send a CV and three confidential letters of reference to: Prof. Haiwei Song (Email: *haiwei(a)imcb.a-star.edu.sg <https://webmail2.imcb.a-star.edu.sg/owa/redir.aspx?C=EzRllkOmnk2jjotDLR8t5a…>*), Institute of Molecular and Cell Biology, A*STAR, Singapore. Cheers, Bharath

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Masked FSC estimation failure
by ze li 13 Oct '19

13 Oct '19

Hello: I have three cryo-ET full maps, not in halves, to estimate their resolutions. I intended to estimate the resolution of the maps with the high-resolution models in the PDB databank. Is it the best to get a map to model FSC estimation at 0.5 cut-off? I calculated three maps with cryo-EM module in Phenix, but only one gives the masked and unmasked curves, the other two only have the unmasked results.I tried many times but failed to figure out the questions of these two maps. What is the possible reason for them? Or Is there any other ways to get the unmasked and masked FSC? Thank you for your help. Sincerely, Ze

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Berkeley Server Outage (Starting October evening 8th)
by Paul Adams 13 Oct '19

13 Oct '19

Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this week meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down today and will return later in the week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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University of Maryland/Open-Rank Tenure-Line Faculty Position
by Hasan, Syed Saif 09 Oct '19

09 Oct '19

Dear Colleagues, The Institute for Bioscience & Biotechnology Research (IBBR) and the University of Maryland, College Park Department of Chemistry & Biochemistry invite applications for an open-rank, tenure-line faculty position in structural biology, with an emphasis in the area of biomolecular cryo-electron microscopy, starting August 2020. A detailed ad is attached to this email. Applications, consisting of a cover letter, curriculum vitae, statement of research plans, statement of educational interests, and three references, must be submitted electronically at: https://ejobs.umd.edu/postings/74094 Review of applications will begin November 15, 2019. We will continue to accept applications until the position is filled. Direct inquiries and/or nominations to the chair of the search committee, at: cryoemsearch(a)ibbr.umd.edu Saif S. Saif Hasan, PhD https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ https://www.ibbr.umd.edu/profiles/s-saif-hasan

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positional restraints in real_space_refine?
by Daniel Larsson 08 Oct '19

08 Oct '19

Hi all, I'm working on a cryo-EM reconstruction where I have some flexible low-resolution elements (RNA double helices). They have different orientations relative to my reference model, but I would like to model them in the approximately correct position. I've tried real_space_refine with morphing and simulated annealing, but neither accomplish what I want. Now I'm thinking of cutting out these helices and manually position them approximately where I want them. But I fear that this will case headache at the "joint". Is it possible to use the manual positions as a reference for positional restraints, but use the original model as the reference for the torsion angles. Is this possible with real_space_refine? Or is there a better way of refining this structure? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Phenix 1.17-3644 installation problems
by Hernando J Sosa 08 Oct '19

08 Oct '19

Dear Phenix developers, Trying to install Phenix in a Linux computer (OpenSuse Leap 15.1)I got the error messages listed below. Any help to fix this problem(s) would be appreciated. Thks. H. Precompiling .py files... Generating SOLVE/RESOLVE license file... Rebuilding HTML documentation... Error rebuilding documentation! Creating rotamer/Ramachandran database files... Traceback (most recent call last): File "./bin/install.py", line 244, in <module> installer(sys.argv[1:]).install() File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 201, in install self.install_finalize() File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 542, in install_finalize self.product_specific_finalize_install(log) File "./bin/install.py", line 130, in product_specific_finalize_install call([os.path.join(self.build_dir, 'bin', 'mmtbx.rebuild_rotarama_cache')], log=log) File "/home/hsxx/Downloads/phenix-installer-1.17-3644-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/hsxx/Programs/Phenix/phenix-1.17-3644/build/bin/mmtbx.rebuild_rotarama_cache' failed with exit code -4

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reference torsion restraints for nucleic acids in real_space_refine
by Daniel Larsson 08 Oct '19

08 Oct '19

Hi all, In phenix.real_space_refine, I'm using a reference model for torsion restraints for a RNA/protein complex. I noticed in the log file under the section "Adding Reference Model Restraints (torsion)" that only the amino acid residues and some modified nucleotides are listed in the "Reference Model Matching Summary" but not the standard nucleotides. Does this mean that they are not restrained? I checked the _initial.geo file and there are no torsion restraints for the standard nucleotides in the "Reference torsion angle restraints" section. Are they not supported by default? My workflow was this: run ready_set on the initial model and then supply real_space_refine with a reference model and the ready_set cif file with the ligands. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Base-pair restraints and high resolution cryoEM maps
by Stephen Cusack 08 Oct '19

08 Oct '19

Dear All, (1) Is it possible to add RNA base-pair restraints into Phenix Real-space-refinement of a lowish resolution cryoEM structure? If so how? (2) We are also lucky enough to have some impressively high resolution cryoEM maps (2.4 A average) which show among other things hundreds of water molecules. I was wondering whether Phenix Real-space-refinement was really adapted to high resolution, e.g. it uses grouped B-factor refinement and has no water handling options (putting them in manually is a pain and you always miss some). How have other people dealt with these issues ? thanks for any help Stephen Cusack -- ********************************************************************** Dr. Stephen Cusack, FRS Head of EMBL Grenoble Group leader in the structural biology of protein-RNA complexes and viral proteins ********************************************************************** Email: cusack(a)embl.fr, stephen.cusack(a)embl.org Website: http://www.embl.fr Tel: (33) 4 76 20 7238 Secretary (33) 4 76 20 7123 Fax: (33) 4 76 20 7199 Postal address: EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue des Martyrs, 38000 Grenoble, France **********************************************************************

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PhD and postdoc position - Structural Biology Methods development at Wuerzburg University
by Andrea Thorn 07 Oct '19

07 Oct '19

Dear colleagues, for two projects in structural biology methods development, we are looking for a PHD CANDIDATE (m/f/d) and a POSTDOCTORAL RESEARCHER (m/f/d) The Thorn Laboratory the Rudolf Virchow Center at the University of Wuerzburg develops new methods for macromolecular X-ray crystallography and Cryo-EM. In these exciting projects you will improve how well we understand, measure and model macromolecular crystal structures using practical experiments and big data analyses. We are looking for candidates with skills in data analysis and programming. Any previous experiences in crystallography, molecular biology, machine learning, image or statistical analysis are also a bonus. You should be a good communicator. For the PhD project, we offer a 36-month full- or part-time position, embedded in the Würzburg Graduate School for Life Sciences (GSLS); for the postdoctoral position, we offer a 30-month full- or part-time position with a competitive salary as well as career and family support. Women are particularly encouraged to apply. For more details, see: https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_PhD_Tho… https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Stellenanzeige_Postdoc… If you have any questions, please email me: andrea.thorn(a)uni-wuerzburg.de. Best wishes, Andrea Thorn. _____ Dr. Andrea Thorn group leader Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany andrea.thorn(a)uni-wuerzburg.de https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/tho…

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Position Available: Crystallography Facility Manager (Research Assistant Professor) - CUNY Advanced Science Research Center, New York City
by Keedy, Daniel 04 Oct '19

04 Oct '19

To the phenixbb community, The Structural Biology Initiative ( https://asrc.gc.cuny.edu/structbio ) of the CUNY Advanced Science Research Center has an available position for an X-ray Crystallography Facility Manager (Research Assistant Professor) starting immediately. The CUNY Advanced Science Research Center is a new cutting-edge research institution located in New York City, bringing together five Initiatives whose research areas span many length scales: Structural Biology, Nanoscience, Photonics, Neuroscience, and Environmental Science. The Structural Biology Initiative (SBI) features seven tenure-track and research faculty members, pursuing research problems across biological and chemical topics using techniques as diverse as X-ray diffraction, cryo-EM, NMR, solution biophysics, and advanced microscopy. The SBI also hosts state-of-the-art core facilities in three different areas: nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry (MS), and X-ray crystallography. The Structural Biology Initiative seeks a Facility Manager/Research Assistant Professor for the X-ray Macromolecular Crystallography Facility, which is already equipped with a Rigaku Alchemist DT liquid handler, two ARI Gryphon crystallization robots, and two Rigaku Minstrel DT crystal imagers at room temperature and 4°C. The selected candidate will be responsible not only for directing day-to-day operations of the facility in concert with users from the ASRC and externally, but also for developing an independent research program that leverages emerging technologies in X-ray crystallography. The ASRC is located in upper Manhattan, immediately adjacent to the New York Structural Biology Center (NYSBC), a consortium of CUNY and eight other New York academic institutions with world-class cryo-EM, NMR, and X-ray facilities on-site and at Brookhaven National Laboratory. BNL, located just 70 miles from the ASRC, includes a newly constructed synchrotron, National Synchrotron Light Source II, which opened in 2015. NSLS-II is now the brightest synchrotron light source in the United State, offering X-rays that are 10,000x brighter than the original NSLS. The ASRC Structural Biology Initiative has access to several cutting-edge microfocus beamlines equipped for automated crystal handling and data collection at NSLS-II, including the NYX beamline via CUNY’s membership in NYSBC and the AMX and FMX beamlines via proposals. Please find more detailed information about the position and officially apply via the following URL: https://cuny.jobs/new-york-ny/macromolecular-crystallization-facility-manag… Review of applications will begin on October 16. Best regards, Daniel Keedy — Daniel A. Keedy, Ph.D. Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center www.keedylab.org<http://www.keedylab.org> | dkeedy(a)gc.cuny.edu<mailto:[email protected]> (NOT @asrc) | 212-413-3246

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Re: [phenixbb] Figure of merit from refinement
by Alexandre OURJOUMTSEV 03 Oct '19

03 Oct '19

Dear Andre, (I repeat here the same message that I've just sent through the ccp4bb; sorry for answering late) I would strongly advice you to look at the article by Lunin and Skovoroda (Acta Cryst, A, 1995) that addresses exactly your question: https://scripts.iucr.org/cgi-bin/paper?vs0124 The authors remind a very important point that after model refinement ML phase errors are strongly underestimated if using all reflections, as that was done in the original works (see references in the article). While the same ML estimates work perfectly for unrefined models, that's not the case for refined ones, as was observed yet in the beginning of 80ths. These authors show then that using the test-set of reflections (the same as for R-free) is crucial to get the correct phase error estimates and respective FOMs for all cases, as this is implemented now in modern refinement programs, e.g. phenix.refine. See also the article by Pannu & Read (Acta Cryst, A, 1996) https://onlinelibrary.wiley.com/doi/pdf/10.1107/S0108767396004370 A more recent important article on this topic is that by Praznikar and Turk (Acta Cryst, D, 2009) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257616/ who discuss what can be done if a statistically significant test set of reflections is not available. I hope this helps you. I am ready to answer you further eventual questions (probably, in a private correspondence). With best wishes, Sacha Urzhumtsev ________________________________ -------- Forwarded Message -------- Subject: [phenixbb] Figure of merit from refinement Date: Tue, 1 Oct 2019 08:15:14 -0300 From: Andre LB Ambrosio <andre(a)ifsc.usp.br><mailto:[email protected]> To: phenixbb(a)phenix-online.org<mailto:[email protected]> Dear all, How is the FOM calculated for a given reflection specifically in the context of model refinement? How useful is it in assessing the phase quality, when not for initial experimental phases? Many thank in advance, -- Andre LB Ambrosio

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