May 2026 - phenixbb - phenix-online.org

Cryo_fit installation
by omar.debei＠unipr.it 06 Jun '26

06 Jun '26

Hi everyone, I was wondering if you could help me with installing cryo_fit on an Ubuntu machine. I followed the instructions here for the cryo_fit installation. Then, I tried to follow this guide to install gromacs_cryo_fit. However, I got stuck at the "Install using a provided script" step. Do I need to install GROMACS separately before proceeding? Any tips would be greatly appreciated! Many thanks, Omar

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Refine partially occupied ligand in active site containing chloride ions
by Stephen.carr＠rc-harwell.ac.uk 06 Jun '26

06 Jun '26

Dear phenix bb, I am trying to refine a ligand in the active site of my protein where the ligand occupancy is ~50%. The empty active site contains two chloride ions and the residual density from these ions is very prominent when the model is refined with the ligand alone. I would like to refine the model with both the ligand and chloride ions present and have been trying to do this with altLoc flags but so far with no luck. I'm assuming that since the Cl ions more-or-less directly overlay atoms from the ligand positional refinement keeps pushing them out of the density. I'm sure there is a simple way to get around this and I would be grateful for any suggestions. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.carr(a)rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.

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AKM in Phenix
by lucas.santosouza＠outlook.com 06 Jun '26

06 Jun '26

Hi everyone, Is there still support for the generation of Average Kick Maps in Phenix? I am using both versions 1.21.2-5419 and the nightly build 2.0rc1-5555. I added kicked=True to the maps.params, but phenix.maps gives me "Unused parameter definitions: maps.map_coefficients.kicked (file "maps.params", line 53)". I also cannot see the "Kicked map" check box in the Create Maps GUI. Cheers, Lucas

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Ion placement (anomalous) + occupancy refinement
by miha.pavsic＠fkkt.uni-lj.si 06 Jun '26

06 Jun '26

Hi everyone, I have a dataset from a protein that contains 2 Ca2+ binding sites. The Ca2+ loaded protein was crystallized in the presence of Tb3+ which at one site mostly replaced Ca2+, however at the other site the Tb3+/Ca2+ ratio appears to be much lower (judging from anomalous map; data collected at 1.3 Å wavelength, MR for phasing). The occupancy sum of Tb3+ and Ca2+ at each of the two sites is strongly believed to be 1. While I am aware of the ion placement option in phenix.refine, I am not so sure how to refine the partial occupancies using anomalous data, if possible. Many thanks for any hints, Miha

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Pdb validation report via phenix
by Stachowski, Tim 06 Jun '26

06 Jun '26

I’ve always found the phenix.get_pdb_validation tool to be super helpful to gauge where my refinements are relative to the PDB, especially since I work mainly through the command line. But sometime around late last year, the R-free metric stopped being calculated (probably related to “EDS: FAILED”). Is there a way to bring this part of the tool back – or does anyone have a work around they can share? I’m running the command like: phenix.get_pdb_validation_report final-coot-3_refine_001.reflections.cif final-coot-3_refine_001.cif with version: phenix-2.0rc1-5599 Thanks Tim -- Tim Stachowski, PhD St. Jude Children’s Research Hospital ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

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.cif file has 'UNK' auth_asym_id
by Kevin M Jude 06 Jun '26

06 Jun '26

I’ve finished refining a structure with three protein chains A, B, C. The pdb file looks ‘normal’ to me, but when I inspect the .cif file written by phenix, the auth_asym_id for chains B and C is ‘UNK’. label_asym_id is correct for all chains. I’m not really sure what the difference is between the auth_ and label_ fields. When I try to perform actions on the .cif file, I get duplicate atom label errors. Here’s a few example lines from the .pdb and .cif files, where auth_asym_id is field 6 and label_asym_id is field 16 ATOM 460 OXT PRO A 59 5.272 55.689 31.481 1.00 52.63 O ANISOU 460 OXT PRO A 59 6541 6212 7244 1448 1260 96 O TER ATOM 461 N ALA B 2 39.292 61.974 39.403 1.00 67.81 N ANISOU 461 N ALA B 2 7118 8729 9916 -1711 -388 2066 N ATOM 460 OXT . PRO A 59 ? 5.27169 55.68852 31.48123 1.000 52.63052 O ? A ? 58 1 ATOM 461 N . ALA UNK 2 ? 39.29207 61.97430 39.40271 1.000 67.80544 N ? B ? 1 1 I’m able to convert the pdb file to a usable cif file using gemmi but wanted to report this weird behavior with phenix 1.21.2_5419. -- 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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Trouble with GTP/GDP refinement.
by DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO 06 Jun '26

06 Jun '26

Dear phenixbb: I'm working with a GTP binding protein and have had some problems running phenix_refine. In my unit cell there are two molecules one with GDP and one with GTP, which I added in Coot(0.9.8). When refining the following error message pops-up : "Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols:4 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modifications and apply_cif_link parameter definitions if necessary". Checking the log file I found that the problem seems to be hydrogen atoms from these ligands Number of atoms with unknown nonbonded energy type symbols: 4 "HETATM 6499 H5' GTP A 501 .*. H " "HETATM 6502 H5'' GTP A 501 .*. H " "HETATM12939 H5' GDP B 501 .*. H " "HETATM12940 H5'' GDP B 501 .*. H " Including the corresponding .CIF files (dowloaded from PDB) did not solve the problem and the same error popped. Since I'm in the initial stages of the refinement I'm running phenix with bindividuals. Could anybody save my day giving me some light into this issue? Cheers, Diego

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CSD changes conformation to planar during phenix.refine
by Andrea Smith 06 Jun '26

06 Jun '26

Hi all, I have a structure where I clearly see that one of the cysteines is oxidised. I have modelled CSD instead of CYS and when I do real space refine in Coot, the CSD sits nicely in the density. When I submit the phenix.refine job, I can see that the geometry changes and now the SOOH is planar. I tried to add the CSD.cif from PDB into phenix.refine as restraints, but it doesn't help and during the automatic refinement the geometry is changed to planar again. Anyone experienced same thing? What do I do? Thank you, Andrea

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seeking help for phenix - coot model building
by tim smith 06 Jun '26

06 Jun '26

Hi everyone, I’m currently working on building a model and have encountered some difficulties with the map-model process. I would greatly appreciate it if anyone could assist me in either helping to build the model or teaching me how to do it. I’m happy to offer a suitable reward for your time and help. Thank you in advance for considering! Regards, Stim

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Issues with zero B-factor and ADP refinement
by sylee00＠snu.ac.kr 06 Jun '26

06 Jun '26

Dear all, I am encountering issues related to B-factors and ADP refinement in Phenix and would appreciate any insights or suggestions. I am currently working on my first PDB file, but I've noticed that many atoms in the PDB file have a B-factor of 0. As far as I understand, B-factor values are calculated by ADP refinement in Phenix real-space refinement, but even after running real-space refinement (with ADP on in refinement settings), the B-factor remains 0 for many atoms. I am currently using Phenix 1.20 on Windows (Newest version available on window). I also attempted to run Phenix 1.21 on a Linux in other computer, but when ADP refinement is enabled, the process starts normally but halts during the ADP refinement step. So I couldn't test whether the issue is fixed in the newest version. Aside from the B-factor issue, I am also experiencing an inssue related to ADP refinement: When I run real-space refinement with ADP refinement enabled, the process starts normally but halts during the ADP refinement step. According to the log file, other refinement steps proceed without issues, but it fails to progress at the ADP refinement stage. Additionally, when I try to pause the process, I receive a "NoSuchProcess" error, so ADP refinement process may have unexpectedly terminated. At first, I thought it's the issue related to system performance or hardware differences, because adp refinement with this pdb file and identical parameters works on some computer but fails on others (the same version of Phenix). Still it's weird because this issue has occurred unexpectedly, as ADP refinement previously worked in my computer under the same conditions without any problems and also other PDB files run without any problems in my computer. I would appreciate any insights or suggestions on how to resolve this. Thanks

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