June 2026 - phenixbb - phenix-online.org

CBMS Lecture Series - Chakraborty - 24 June 2026
by Stojanoff, Vivian 18 Jun '26

18 Jun '26

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Saumen Chakraborty The University of Mississippi WEDNESDAY, June 24, 13:30 (EDT) "Artificial Metalloproteins to Harvest Solar Energy and Small Molecule Activation" Register in advance for this meeting: https://bnl.zoomgov.com/j/1608968233?pwd=zJn5FYvcPM58P1CfantsS6bhTiMIIW.1 Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: Metalloenzymes catalyze complex reactions with unprecedented efficiency. These enzymes are promising candidates for various biotechnological applications, including producing alternative fuels and pharmaceuticals. Oftentimes, the innate complexity of these metalloenzymes prohibits a true appreciation of their full capability and a detailed understanding of their structure-function relationships. One approach to alleviating this issue is to design artificial metalloenzymes (ArMs) that still contain the metal of interest in a biomolecular environment, allowing the chemistry to be performed in aqueous media. The protein scaffold prevents unwanted side reactions. In addition, the protein environment allows one to alter outer sphere interactions to fine-tune their reorganization energies and reactivity. In this seminar, I will present two complementary approaches to designing Ni and Cu-containing ArMs – artificial hydrogenases and artificial C-H peroxidation catalysts utilizing protein reengineering and de novo protein design approaches.

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Creating a bond between symmetry mates on phenix
by Ezennubia, Purity 11 Jun '26

11 Jun '26

Hello everyone, I am new to this forum and I am glad this exists for discussions between phenix users. I have been trying to create a bond between two atoms belonging to different symmetry but when I create the bond restraints on phenix, I get an error message that says custom bonds with excessive length and I later realized the problem is not the bond length but the fact that the two atoms are in different symmetry. Is there a way to make this work on phenix? I would love suggestions on this. Thank you, Purity

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comprehensive validation (cryoem)
by Roberto Marabini 11 Jun '26

11 Jun '26

Hi, We are using the Phenix protocol "Comprehensive Validation (CryoEM)" (version 2.0.5936). The input structure file is provided in mmCIF format. We have observed that the protocol fails when chain IDs contain three characters, whereas it completes successfully when chain IDs contain two characters. Based on this behavior, we suspect that the protocol may internally convert the input mmCIF file to the legacy PDB format. Could you please confirm whether this assumption is correct? If such a conversion is performed internally, we would also like to understand how the protocol handles structures that exceed the limitations of the PDB format, for example files containing more than 99,999 atoms or chain identifiers that are not supported by the traditional PDB specification. When the protocol fails the following warnings are reported: Bad HELIX record, was skipped: HELIX 1 1 MET0Ah 7 HIS0Ah 14 1 8 Bad HELIX record, was skipped: HELIX 2 2 SER0Ah 25 GLU0Ah 36 1 12 ... Bad sense in SHEET record: '9' Thank you for your help. Best regards, Roberto

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GUI installer for Phenix crashes after 15 minutes
by Mark Saper 08 Jun '26

08 Jun '26

I have an Intel MacBook Pro running macOS 15.7.7. I downloaded the appropriate GUI installer for Phenix 2.1. The installation runs for about 15 min and then fails with a vague message. This happened to me previously with Phenix 2.0. I used the command line installer in each case and that was successful. I reported the problem but I received no response. Can the GUI installers be fixed? Thanks, Mark _____________________ Mark A. Saper, Ph.D. Visiting Professor Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

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new BUILT of XDS
by kay.diederichs＠uni-konstanz.de 06 Jun '26

06 Jun '26

Dear XDS users in the Phenix community, as reported by users, and confirmed in a larger-scale comparison by GlobalPhasing, the BUILT=20240723 of XDS Version 20240630 leads to problems for some datasets when compared with (the expired) XDS Version 20230630. (it may be better than the 20230630 version for other datasets!). An improved BUILT=20241002 of the 20240630 version is available (all platforms) from https://xds.mr.mpg.de/html_doc/downloading.html for non-commercial (academic) users (commercial users have their own arrangements). In my/our testing, it is at least as good as version 20230630, and often better. Please install and use this instead of BUILT=20240723. If you still find deficiencies, please contact me or Wolfgang Kabsch - but be prepared to share the raw data (confidentially, of course). To enable comparisons, the old XDS version 20230630 was re-released for Linux by Wolfgang Kabsch with expiration date 2025-Mar-31; the link to its XDS_old.tar.gz is at https://xds.mr.mpg.de/ . Best wishes, Kay

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real space refine ADPs
by Leonid Sazanov 06 Jun '26

06 Jun '26

Hi, according to online description phenix.real_space_refine should refine only group ADPs per residue. However, in practice after the run with ADP included in strategy the recent versions refine individual B-factors per atom. They seem to look OK, but I wonder if this is a beta feature or fully implemented by now? Many thanks Leonid -- Prof. Leonid Sazanov FRS Institute of Science and Technology Austria (ISTA) Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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Temperature shift alters unit cell of insulin: an issue
by Esra A 06 Jun '26

06 Jun '26

Dear Phenix community, I performed a temperature shift data collection for di-hexamer insulin. I collected single crystal data at 100K, 200K, and 300K, respectively After processing the data, I noticed that the unit cell of the 100K dataset is distinct from 200K and 300K. 100K dataset = 78.2182 78.2182 79.3565 90 90 120 (assume that this is di-hexamer) 200K dataset = 78.3157 78.3157 39.6367 90 90 120 (it is hexamer) 300K dataset = 80.7109 80.7109 39.6399 90 90 120 (it is hexamer) Even if I completed the structure determination of 200K and 300K successfully, I couldn't complete the molecular replacement of the 100K dataset due to the "*The composition entered will not fit in the unit cell volume*" error message. I tried every "copies" and "mass" parameter in *automr *script. However, i got the error message every run. I can share with you the mtz and reference pdb file, if needed. Could you help me, please? Where am I making a mistake? Thank you very much. Sincerely, Esra Ayan

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Building Rosetta for Phenix
by Martin Malý 06 Jun '26

06 Jun '26

Dear colleagues, I am dealing with a low resolution data set (~4 A, protein crystal structure) so I would like to explore phenix.rosetta_refine. I followed the instructions at https://phenix-online.org/documentation/reference/rosetta_install.html . I applied the patch in ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings . After several minutes of compilation (command rosetta.build_phenix_interface), I got an error. I re-run the command to get a log file which I'm attaching. Please don't you have any idea what's wrong? I use Ubuntu 22.04. Thank you. Best regards, Martin

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help for the 4.3 A dataset
by princeadam＠163.com 06 Jun '26

06 Jun '26

Dear colleagues, I am currently engaged in an endeavor to unravel the crystal structure through molecular replacement techniques. Regrettably, the resolution attained stands at a rather low mark, approximately 4.3 Angstroms, which poses significant challenges. Despite exhaustive efforts directed towards optimizing the crystal conditions, there has been no discernible improvement in the resolution. The structure in question is confined to a specific domain, and we have at our disposal two distinct conformational models sourced from the PDB database: one derived from X-ray data and the other from Cryo-EM. Our prime objective is to meticulously discern which of these two conformations aligns most accurately with our experimental context. To this end, we have employed both structures (X-ray and Cryo-EM) as templates for molecular replacement, yet the refinement process has hit a roadblock, hindering our progress. We are seeking a collaborator with experience in dealing with low-resolution data to assist in solving the structure. We are open to sharing first or corresponding authorships in the near future for this paper. Warm regards Hui

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AQuaRef - issues with torch-cluster installation
by Martin Malý 06 Jun '26

06 Jun '26

Dear colleagues, I'm trying to install AQuaRef. However, I'm struggling with running `bash config/update_phenix.sh aimnet2` which is part of `bash build_into_phenix.sh aimnet2`. This script wants to install the python package torch-cluster. However, I'm getting the error: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] I'm getting the same error when I tried to install only this package using the command `qrefine.python -m pip install torch-cluster`. I have a laptop with Ubuntu 22.04. I have all the usual development packages installed (build-essential, linux-headers, gcc, g++, ...). According Python, I have libpython3-dev, libpython3.10-dev, python3-dev, python3.10-dev. I can see that qrefine.python has a version of 3.9, so I also installed libpython3.9-dev, python3.9-dev and python3.9-distutils from ppa:deadsnakes/ppa but it did not help. I am also attaching a full log from the torch-cluster installation. It seems that the package torch has been installed successfully in prior. Do you have please an idea what is wrong and how to fix it? Thank you. Martin

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