- phenixbb - phenix-online.org

sub-unitary occupancy group restraints sum
by Kreitler, Dale 17 Apr '25

17 Apr '25

Hi, For refining an x-ray structure which has a ligand bound with multiple poses modeled as alternate confirmations, is there a way in phenix refine to maintain that the occupancy of each conformation is equal while allowing the sum total occupancy to vary (rather than equal 1)? I realize the [0,1] min/max occupancy values are adjustable parameters -- my interpretation of the docs is that this is not possible, but I thought it'd be worth asking. An example might be a ligand bound with partial occupancy near a rotational symmetry axis. Thank you, Dale ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318

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twinning and translational NCS issues
by Wenhui Xi 16 Apr '25

16 Apr '25

Hi all, i have this crystal which was reported severe issues with twinning and translational NCS, thus when i tried to refine its structure, the Rfree would go up to nearly 60% which making directly solving its structure very hard. i'm writing to ask are there any helpful ways to deal with this issue? Thank you! Joyce [image: image.png]

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CBMS Structural Biology Workbench - May 27 through 30, 2025 - registration deadline April 15
by Stojanoff, Vivian 14 Apr '25

14 Apr '25

Dear Colleagues, The CBMS Structural Biology Workbench will take place May 27 through 30, 2025. The first two days, May 27 and 28, are dedicated to MX and the following days May 29 and 30 to Solution Scattering and X-ray Footprintig. This is an IN-PERSON workshop. DEADLINE to REGISTER APRIL 15 https://www.bnl.gov/cbmsworkbench/ PROGRAM Macromolecular Crystallography May 27 - MX data collection on participants samples and pre-analysis May 28 - Phenix workshop "The Phenix workshop will focus on crystallographic refinement using phenix.refine. The first lecture will introduce major features and best practices of reciprocal space refinement, followed by a basic tutorial demonstrating how to run phenix.refine with default options. The second lecture will cover strategies for low-resolution refinement, including the use of secondary structure restraints and reference models. Participants who so desire will have the opportunity to work on their own data with Phenix developers available to answer questions—on phenix.refine or any other Phenix tools in the afternoon. Solution Scattering - SAXS & Xray Footprinting - XFP May 29 - Introduction to SAXS & LIX; Data collection on participants samples May 30 morning - SAXS data analysis software May 30 afternoon - Introduction to XFP and hands-on tutorial Questions can be directed to Vivian Stojanoff (stojanof(a)bnl.gov). ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?…>

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Re: phenixbb Digest, Vol 232, Issue 13 (out of office)
by Elisabeth Laurent 13 Apr '25

13 Apr '25

Thank you for your e-mail. I am out of office until April 23rd, 2025. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: bmca(a)boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> <phenixbb-request(a)phenix-online.org> 13.4.25 20:51 >>> Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: Question about geometry outliers in RealSpaceRefine (Pavel Afonine) 2. Re: DEN restraints and ECHT disorder models (Tom Burnley - STFC UKRI) ---------------------------------------------------------------------- Message: 1 Date: Fri, 11 Apr 2025 11:47:11 -0700 From: Pavel Afonine <pafonine(a)lbl.gov> Subject: [phenixbb] Re: Question about geometry outliers in RealSpaceRefine To: Kevin M Jude <kjude(a)stanford.edu>, "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Message-ID: <7968370b-7470-4fe4-aaf1-052661202ef9(a)lbl.gov> Content-Type: multipart/alternative; boundary="------------YozFq5Oyt0xmhpmEfOqMdIo0" Hi Kevin, could you please send me the file (off list)? Thanks! Pavel On 4/11/25 09:34, Kevin M Jude wrote: > > After a recent RealSpaceRefine run, the Geometry Restraints tab in the > gui reports that I have two bond angle outliers > 4 sigma, but only > lists one of them: > > D 180 MET N, D 180 MET CA, D 180 MET CB 114.170 109.342 4.2 > > So I check the logfile for the job and see: > > Bond angle restraints: 12582 > > Sorted by residual: > > angle pdb=" N MET D 180 " > > pdb=" CA MET D 180 " > > pdb=" CB MET D 180 " > > ideal model delta sigma weight residual > > 114.17 109.34 4.83 1.14e+00 7.69e-01 1.79e+01 > > angle pdb=" CA LEU B 79 " > > pdb=" CB LEU B 79 " > > pdb=" CG LEU B 79 " > > ideal model delta sigma weight residual > > 116.30 127.81 -11.51 3.50e+00 8.16e-02 1.08e+01 > > angle pdb=" C ASP B 333 " > > pdb=" N SER B 334 " > > pdb=" CA SER B 334 " > > ideal model delta sigma weight residual > > 122.74 127.19 -4.45 1.44e+00 4.82e-01 9.54e+00 > > angle pdb=" C GLN D 167 " > > pdb=" N ARG D 168 " > > pdb=" CA ARG D 168 " > > ideal model delta sigma weight residual > > 121.48 126.80 -5.32 2.04e+00 2.40e-01 6.80e+00 > > angle pdb=" C ASP B 163 " > > pdb=" N THR B 164 " > > pdb=" CA THR B 164 " > > ideal model delta sigma weight residual > > 123.47 127.30 -3.83 1.53e+00 4.27e-01 6.27e+00 > > ValidationCryoEM returns identical results except the gui says only > one > 4-sigma outlier (at //D/Met180/). PDB Validation reports only > the outlier at //B/Leu79/, which does have the largest sigma in the > above log. > > My questions are: > > 1. Why does the gui report two 4-sigma outliers but only show one? > 2. Why do the sigmas in the log file not correspond to the sigmas in > the gui? > > Best wishes > > Kevin > > -- > > Kevin Jude, PhD > > Structural Biology Research Specialist, Garcia Lab > > Howard Hughes Medical Institute > > Stanford University School of Medicine > > Beckman B177, 279 Campus Drive, Stanford CA 94305 > > > _______________________________________________ > phenixbb mailing list --phenixbb(a)phenix-online.org > To unsubscribe send an email tophenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s

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DEN restraints and ECHT disorder models
by Roberto Battistutta 13 Apr '25

13 Apr '25

Dear all, From which version of Phenix are the DEN restraints and ECHT disorder models implemented in the ensemble refinement (as described in Ploscariu, N., Burnley, T., Gros, P. & Pearce, N. M. (2021). Improving sampling of crystallographic disorder in ensemble refinement. Acta Cryst. D77, 1357-1364)? Thank you very much, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistutta(a)unipd.it

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Question about geometry outliers in RealSpaceRefine
by Kevin M Jude 11 Apr '25

11 Apr '25

After a recent RealSpaceRefine run, the Geometry Restraints tab in the gui reports that I have two bond angle outliers > 4 sigma, but only lists one of them: D 180 MET N, D 180 MET CA, D 180 MET CB 114.170 109.342 4.2 So I check the logfile for the job and see: Bond angle restraints: 12582 Sorted by residual: angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 114.17 109.34 4.83 1.14e+00 7.69e-01 1.79e+01 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 127.81 -11.51 3.50e+00 8.16e-02 1.08e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 127.19 -4.45 1.44e+00 4.82e-01 9.54e+00 angle pdb=" C GLN D 167 " pdb=" N ARG D 168 " pdb=" CA ARG D 168 " ideal model delta sigma weight residual 121.48 126.80 -5.32 2.04e+00 2.40e-01 6.80e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 127.30 -3.83 1.53e+00 4.27e-01 6.27e+00 ValidationCryoEM returns identical results except the gui says only one > 4-sigma outlier (at //D/Met180/). PDB Validation reports only the outlier at //B/Leu79/, which does have the largest sigma in the above log. My questions are: 1. Why does the gui report two 4-sigma outliers but only show one? 2. Why do the sigmas in the log file not correspond to the sigmas in the gui? Best wishes Kevin -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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Simulate map from model
by Ricardo Righetto 10 Apr '25

10 Apr '25

Hi, Apologies if I'm missing something obvious, but I was not able to find this in the documentation: is there a PHENIX tool for simulating Coulomb potential maps (aka "cryo-EM maps") from atomic models? I'm looking for something like the molmap <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> command in ChimeraX, but more accurate. One such alternative is the simulate program from cisTEM, but I figured PHENIX might also have something? Thank you! -- Ricardo Diogo Righetto

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Differential density peaks and hydrophobic residues
by Lucas Souza 04 Apr '25

04 Apr '25

Hi everyone, I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied). Does anyone have a guess about that? Best, Lucas -- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000

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CBMS Structural Biology Workbench - May 27 through 30, 2025 - registration deadline approaching
by Stojanoff, Vivian 03 Apr '25

03 Apr '25

Dear Colleagues, The CBMS Structural Biology Workbench will take place May 27 through 30, 2025. The first two days, May 27 and 28, are dedicated to MX and the following days May 29 and 30 to Solution Scattering and X-ray Footprintig. This is an IN-PERSON workshop. DEADLINE to REGISTER APRIL 15 https://www.bnl.gov/cbmsworkbench/ PROGRAM Macromolecular Crystallography May 27 - MX data collection on participants samples and pre-analysis May 28 - Phenix workshop "The Phenix workshop will focus on crystallographic refinement using phenix.refine. The first lecture will introduce major features and best practices of reciprocal space refinement, followed by a basic tutorial demonstrating how to run phenix.refine with default options. The second lecture will cover strategies for low-resolution refinement, including the use of secondary structure restraints and reference models. Participants who so desire will have the opportunity to work on their own data with Phenix developers available to answer questions—on phenix.refine or any other Phenix tools in the afternoon. Solution Scattering - SAXS & Xray Footprinting - XFP May 29 - Introduction to SAXS & LIX; Data collection on participants samples May 30 morning - SAXS data analysis software May 30 afternoon - Introduction to XFP and hands-on tutorial Questions can be directed to Vivian Stojanoff (stojanof(a)bnl.gov).

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for autobuild full sequence?
by James Holton 03 Apr '25

03 Apr '25

Hey all, Don't worry, nothing is funny today. I have a real question: Is there a way to force phenix.autobuild to build in the entire sequence? As in: the full length of the actual molecule that is in the crystal, such as what is supposed to go into SEQRES, regardless of "visible" density? I am trying to come up with a pipeline for prepping MD simulations of protein crystals. It seems proper to me that the molecule being simulated should be the actual molecular species, disordered bits an all. However, we don't seem to have good technology for building protein chains into "nothingness". Yes, I know Alphafold is a thing, but it is rubbish at clashes in the context of a crystal. I mean, I could write something, but does this tool already exist? Cheers, and happy Tuesday, -James Holton MAD Scientist

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