- phenixbb - phenix-online.org

Amber force field for phenix.real_space_refinement?
by Sebastian Eustermann 24 Jan '18

24 Jan '18

Dear All, I just wondered whether/how one can use the Amber force field also for phenix.real_space_refinement? I tried “use_amber=True” as it is implemented for phenix.refine but that option does exists for phenix.real_space_refinement … Thanks for your help BW Sebastian -------------------------------------- Sebastian Eustermann, PhD Gene Center LMU Munich, Germany

2 1

phenix.auto_sharpen expected filtration of input map
by Ricardo Righetto 24 Jan '18

24 Jan '18

Hi, So far I have liked very much the results of phenix.auto_sharpen, but one thing is not yet clear to me: how does it expect the input map to be filtered? Would be something like: a) Unsharpened, unfiltered map (e.g. the simple average of the half-maps) b) Unsharpened, SSNR-weighted (Cref) (Rosenthal & Henderson, JMB 2003) c) Doesn't matter / other? Thanks in advance! Best wishes, -- Ricardo Diogo Righetto

2 2

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

3 2

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

2 1

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 ******************************************************

3 3

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

2 1

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)

1 0

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

2 1

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

18 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

3 4

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

2 5