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Error with Phenix refine after adding ligand
by Mian-Chee Gor 23 Jan '18

23 Jan '18

Hello all, I run into this problem when I tried to refine my protein structure after adding ligand. The ligand that I am adding is a malonate, and the 3-letter chemical code is MLI. I add the ligand using Coot and it fit perfectly into the electron density map. I then tried to run phenix.refine by giving the protein structure pdb file, the original mtz file and the protein sequence fasta file. However, there was an error message saying missing restraints for the ligand. So I generate the CIF file for the ligand using the Ready Set icon in the toolbar. The ligand CIF file and a updated protein structure pdb file was generated and automatically added to the refinement windows. However, when I run the refinement, I saw this error message: Number of nonbonded interaction distances <0.001:2. Please inspect the output above (or in the log window) and correct the input model file. When I inspect the log window, the error is due to the oxygen atoms in the ligand being too close to each other. Why is there an error if the ligand was generated automatically in Phenix? Has anyone encounter this problem before? How do you solve that? Many thanks in advance! -- Dr Mian-Chee Gor Research Fellow Griffith Institute for Drug Discovery (GRIDD) Don Young Road, Nathan, QLD 4111 Mobile: +61 4 2084 7785 Email: m.gor(a)griffith.edu.au

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Neutron diffraction protein refinement with Phenix
by Rex Palmer 22 Jan '18

22 Jan '18

I would like to contact someone based in or near London whois familiar with Phenix refinement of neutron diffraction protein structures and interpretation of the results. Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7

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secondary structure presentation in VMD
by CPMAS Chen 22 Jan '18

22 Jan '18

Hi, Phenix users, This may be a little off-topic. I have posted this in VMD users mail list. I want to try here too to see if anyone experienced similar issue. VMD and pymol gave different presentation on the secondary structure of a protein. During phenix.refinement, I added secondary structure restraints and correctly labelled all helices and sheets. However, VMD does not correctly present the secondary structure in cartoon/new-cartoon presentation. A little more detail. In VMD-1.9.4a12, after I loaded the pdb, I chose new cartoon to present the secondary structure. All chains are presented as random coil, the same as tube representation. However, pymol correctly shows the secondary structure of the same pdb file in cartoon representation. Has anyone encountered similar situation? what would be the fix? Thanks! Best Regards, Charles -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Refining a neutron structure
by Rex Palmer 19 Jan '18

19 Jan '18

When refining a neutron structure with Phenix why would the program appear to think it was an X-ray structure? Rex Palmer http://www.bbk.ac.uk/biology/our-staff/emeritus-staff http://www.springer.com/978-1-4641-3954-7

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XChem compound design: recruiting programmer / software engineer
by Frank von Delft 19 Jan '18

19 Jan '18

Dear MXers We are recruiting a software engineer (or scientific programmer, or geek-minded scientist, or scientifically-minded geek) to help us get a lot better at designing compounds from hits from crystallographic fragment screening. The post is linked to the XChem facility <http://www.diamond.ac.uk/Beamlines/Mx/Fragment-Screening.html> at Diamond's beamline I04-1, set up in partnership with the SGC-Oxford, which is now routinely hosting users every week, allowing them to find convincing fragment hits with a few days' worth of experiments. In 2017, over 30 users measured over 35,000 crystals in academic and industrial XChem experiments. To confront the next bottleneck, namely converting low potency fragments into high-potency compounds, we are setting up a suite of easily accessible computational tools that streamline the obvious yet surprisingly fiddly analyses by which to identify the most sensible follow-up compounds that are easy to make or procure. The (initially) two-year post will, in a team of three and depending on interests, build infrastructure, harden existing algorithms or help evolve new ones, do web interface design, or any combination of the above. The project is seeding a nascent effort, for now aspirationally code-named CCP-CMC (/CompMedChem/, http://www.ccp-cmc.org/), to bring the awesome collaborative ethos of CCP4 and other MX tools to computational medicinal chemistry. Recruitment details are here <https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.disp…>. Deadline is Monday 29 Jan (it's wrong in the link). -- Prof Frank von Delft 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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Calculate F/sigma(F)
by Cygler, Miroslaw 19 Jan '18

19 Jan '18

Hi, I would like to calculate distribution of F/sigma(F) as a function of resolution for reflections in an mtz file. Is it possible to do it Phenix? Thanks, Mirek

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Re: [phenixbb] Fourier_shell_correlation_(FSC)_in_cryo-EM_refinement
by Takanori Nakane 19 Jan '18

19 Jan '18

Hi Oleg, Do you mean FSC between a model and a map? You can calculate it with phenix.model_vs_map. Best regards, Takanori Nakane > I started to do some refinements of cryo-EM structures. But I could not > find FSC (e.g. FSC average) quality metrics in the refinement log. Is it > because of the real space refinement methodology or some features need to > be activated? Please advise > Thanks > Oleg ? > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org

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Local sharpening error
by Ricardo Righetto 18 Jan '18

18 Jan '18

Hi, I am trying to do local sharpening with phenix.auto_sharpen, with the following command: phenix.auto_sharpen map.mrc resolution=4.0 local_sharpening=True Then it runs the global sharpening first as expected, but when it gets to the local sharpening it crashes with the following error: Sorry: Please specify a sequence file with seq_file=myseq.seq Nowhere it says that I would need a .seq file in order to do local sharpening (global sharpening works fine). Any ideas? Thanks, -- Ricardo Diogo Righetto

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Autobuild in to "extra density"
by Tom Terwilliger 18 Jan '18

18 Jan '18

Hi Ben, I think you've done the hard part already by building a poly-ala model into your extra density! If you want to try and sequence it using the density, you can use phenix.replace_side_chains with the keyword "sequence_from_density=True" to do this. See: https://www.phenix-online.org/documentation/ reference/replace_side_chains.html To use autobuild with this, add an extra line to your sequence file with the sequence of the extra piece (separate it from the previous sequence with a blank line or a ">".) I would try rebuild_in_place=True to try and optimize the position of your extra chain. You can specify what residues to work on with something like: rebuild_chain_list=A rebuild_res_start_list=27 rebuild_res_end_list=35 This will rebuild chain A27 through A35. For density modification you might want to use a mask based on your model. For this you would say: mask_from_pdb=my_existing_pdb_file.pdb Let me know if that doesn't do it! All the best, Tom T Date: Tue, 9 Jan 2018 20:50:41 +0000 From: "Flath, Ben" <bef206(a)mail.usask.ca> To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Autobuild in to "extra density" Message-ID: <52cba352941e48869fc9d5223a97ccaf(a)Mail06.usask.ca> Content-Type: text/plain; charset="us-ascii" Hi All I have a structure I am building/refining at 2.6 A resolution, there are three NSC molecules in P321 unit cell. Each monomer contains 150 aa and are at least 95% built. Here is where I need some help. There is extra density. Gel and Mass Spec data suggests that there is a smaller MW weight protein/band contained in the crystals which is most likely a fragment of my target protein. Basically I have 3 NCS copies plus a half a molecule that does not appear to have the same tertiary structure (LSQ & SSM do not align well) as the other 3 molecules. I have been able to build several poly-A helices in to this density and R/Rfree are now 0.25/0.31. My Question is, how do I set up a phenix run (presumably autobuild) So that I can begin to dock my sequence in to these chains and have them extended? Does my sequence input file need to include more than one sequence string? Asking autobuild to find and build 4 NCS groups does not seem to build anything in to this extra density (Also the sigma level for the extra density chains seems to be somewhat less than the well-defined part) I am guessing this is a rebuild_in_place=false job? Can I specify only a certain chain only to be rebuilt? Also are there some special considerations with regard to density modification I should be aware of? Any help would be much appreciated. Regards Benjamin Flath, M.Sc. Research Assistant, Cygler Lab University of Saskatchewan Department of Biochemistry Room 3D40 HSCI Box 27, 107 Wiggins Road Saskatoon, SK S7N 5E5 Phone: 306 220-7355 email: benjamin.f(a)usask.ca<mailto:[email protected]> -- 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: 505-431-0033

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Fourier shell correlation (FSC) in cryo-EM refinement
by oleg＠quantumbioinc.com 18 Jan '18

18 Jan '18

I started to do some refinements of cryo-EM structures. But I could not find FSC (e.g. FSC average) quality metrics in the refinement log. Is it because of the real space refinement methodology or some features need to be activated? Please advise Thanks Oleg

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