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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 12 Sep '21

12 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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NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September
by Randy John Read 27 Aug '21

27 Aug '21

Hi, I’ve just learned that this online workshop is generally open, not just to members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s free! Information, including the current programme and a link to registration, can be found here: https://www.nora.ai/events/AlphaFoldv2.0-and-RoseTTAFold-workshop%20.html I’ll be talking a bit about experiences with models from AlphaFold2 and RoseTTAFold, but the real draw should be talks by people who really understand these two deep learning algorithms: Minkyung Baek (first author on the RoseTTAFold paper, from David Baker’s group) and a representative of the DeepMind team that developed the two versions of AlphaFold. Sameer Velankar will also be there to talk about the exciting new AlphaFold database at the EBI. Best wishes, Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Re: [phenixbb] NORA workshop on AlphaFold2 and RoseTTAFold, 31 August and 1 September
by Randy John Read 27 Aug '21

27 Aug '21

9 am CEST (Norway). Pretty early for our North American colleagues, especially those on the west coast! > On 27 Aug 2021, at 05:18, Robert Rose <rbrose2(a)ncsu.edu> wrote: > > Does the workshop start on August 31 at 9 am GMT? > > On Thu, Aug 26, 2021 at 2:27 PM Randy John Read <rjr27(a)cam.ac.uk> wrote: > Hi, > > I’ve just learned that this online workshop is generally open, not just to members of the Norwegian Artificial Intelligence Consortium (NORA), and it’s free! Information, including the current programme and a link to registration, can be found here: > > https://www.nora.ai/events/AlphaFoldv2.0-and-RoseTTAFold-workshop%20.html > > I’ll be talking a bit about experiences with models from AlphaFold2 and RoseTTAFold, but the real draw should be talks by people who really understand these two deep learning algorithms: Minkyung Baek (first author on the RoseTTAFold paper, from David Baker’s group) and a representative of the DeepMind team that developed the two versions of AlphaFold. Sameer Velankar will also be there to talk about the exciting new AlphaFold database at the EBI. > > Best wishes, > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building Fax: +44 1223 336827 > Hills Road E-mail: rjr27(a)cam.ac.uk > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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Peptide bond to symmetry related molecule
by Damian Ekiert 23 Aug '21

23 Aug '21

Hi All, We are refining several structures in which the N-terminal residue of chain A appears to form a peptide bond to the C-terminal residue of its symmetry mate, chain A. In reality, the target protein consists of 4 identical helical repeats that pack end to end. Slippage and averaging over the 4 possible registers leads to the appearance of an infinitely long polymer in the crystal, with no breaks between protomers. Is it possible to enforce a peptide bond to symmetry mates in Phenix, and what is the easiest way to do this? I have found a several cases in the archives on how to deal with symmetry clashes, but struggling to figure out how to deal with a peptide bond. Thanks for your help! Best, Damian - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Damian Ekiert Assistant Professor Skirball Institute | NYU School of Medicine Depts. Cell Biology and Microbiology damian.ekiert(a)ekiertlab.org www.bhabhaekiertlab.org

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