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Today is the last day to register for the SSRL/LCLS User Meeting
by Mooers, Blaine H.M. (HSC) 17 Sep '21

17 Sep '21

Dear Phenixbb: Today is the last day to register for the SSRL/LCLS User Meeting that starts on Monday. It is free and virtual. https://events.bizzabo.com/SLAC-UsersMeeting-2021/home. The poster session runs 12 - 1 PM Pacific Time M-Th. You use the gathertown software to attend it. Navigation of the poster session is like playing a 1990s computer game. I was on the poster judging team. We spent this week judging the posters virtually. We made our selections of the seven poster prize finalists today. All of the semifinalist posters were excellent. Best regards, Blaine SSRL UEC member and past chair. Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

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(no subject)
by Smita Yadav 17 Sep '21

17 Sep '21

Dear All, hello to everyone. I wanted to know which gromac version is mostly used for simulation in linux. -- With Regards Smita Yadav

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NIH-funded Postdoc, Membrane Protein Structural Biology (Nebraska, USA)
by Alex Vecchio 14 Sep '21

14 Sep '21

Dear Phenix Community, I would like to bring your attention to an NIH-funded Postdoc position in the Vecchio Lab <https://vecchio-lab.unl.edu> at the University of Nebraska studying membrane proteins and membrane protein assemblies using X-ray crystallography and cryoEM. We are looking for a recent or soon-to-be Ph.D., with experience in membrane proteins and one structural technique. Potential exists for the candidate to *acquire cryoEM expertise* during the postdoc training via a recently well-scored NSF fellowship. For more information, please read our ad HERE <https://jobrxiv.org/job/vecchio-lab-at-university-of-nebraska-27778-postdoc…> . To apply or for specific questions, please contact me at avecchio(a)unl.edu. All the best, Alex -------------------------------------------- Alex J. Vecchio, Ph.D. *Assistant Professor* University of Nebraska–Lincoln Department of Biochemistry Center for Integrated Biomolecular Communication 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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Assistant Researcher Senior Position in the KU Protein Structure Laboratory
by Lovell, Scott W 13 Sep '21

13 Sep '21

The Protein Structure and X-ray Crystallography Laboratory (PSXL) at the University of Kansas (KU) is seeking a full-time Assistant Researcher Senior to work on a variety of structural biology projects. As a core laboratory, the PSXL collaborates with multiple investigators to obtain structures of their proteins of interest using X-ray crystallography and delivers dozens of structures annually. Additionally, the PSXL is involved in NIAID funded R01 grants and manages the structural biology efforts for projects aimed at antiviral inhibitor development. As such, this position will involve structural biology work to facilitate the structure-guided development of inhibitors targeting the MERS-CoV and SARS-CoV-2 main proteases. For a full description of the position and to apply, GO TO: https://employment.ku.edu/staff/20030BR Regards, Scott __________________________________________________ Scott Lovell Ph.D., Director Protein Structure and X-Ray Crystallography Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 email: swlovell(a)ku.edu<mailto:[email protected]> phone: 785-864-3772 fax: 785-864-8141 https://psxl.ku.edu/ __________________________________________________

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Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 13 Sep '21

13 Sep '21

Hi all, I'm using phenix.real_space_refine to refine a model into a cryo-EM map. My local map resolution is highly variable across the molecule, and using a single map weight (the parameter shown in the Refinement Settings > "Other Options" in the GUI) on the whole model leads to poor map-to-model fit in some locations and overfitting in others. Potential solutions could be to: 1. assign different map weights to different segments of the model (based on a user-specified atom selection) OR 2. perform iterative refinements with different weight settings, holding different (user-specified) segments of the model fixed during each iteration (I suspect this isn't possible based on Pavel's message here: http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) Is either of these approaches (or another one that accomplishes the same goal) possible? I am using the Phenix GUI, but if this is only possible in command line, and you're willing to share an example command that accomplishes either of these tasks, please let me know. Thanks! -Josh (also, apologies if this is a duplicate message...still trying to figure out the phenixbb listserv)

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Extending a structure
by E Artikis 10 Sep '21

10 Sep '21

I have a pdb with a fibril composed of three identical chains. I'd like to expand the fibril from three to 15 chains. Is there a way to do this? It's essentially a copy/paste action, but I can't figure it out. Thanks!

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Phenix opens COOT but does not load map or model
by Boniecki, Michal 08 Sep '21

08 Sep '21

Hello, I used to be able (with previous phenix versions) load models into COOT after refinement. Now when I click open in COOT, only COOT window is open but neither maps or model are loaded.Also there is no "connected to phenix' displayed in COOT sidebar I have no problems with loading and displaying both in phenix or pymol (open with phenix or open with pymol buttons). Any suggestions how to solve it would be appreciated. COOT 0.9.5, phenix 1.19.2-4158 Michal

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Job posting: Scientist (crystallography) at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 08 Sep '21

08 Sep '21

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist with experience in protein chemistry and structural biology (crystallography). The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-protein and 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 8560 Progress Drive, C1012, Frederick, MD 21701 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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IUCr’s Committee on Data recent meeting minutes now online
by John R Helliwell 06 Sep '21

06 Sep '21

Dear Colleagues, I imagine that you will be interested in the IUCr’s Committee on Data recent meeting minutes which are now online here:- https://forums.iucr.org/viewtopic.php?f=39&t=441 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman IUCr Committee on Data

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copy R-free array from reference mtz using command line?
by Aaron Thompson 30 Aug '21

30 Aug '21

PhenixBB, I know this can be done via GUI, but is it possible to copy the R-free array from a reference mtz to a new mtz using the command line? I don’t see this as an option in phenix.reflection_file_converter. Thank you, Aaron

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