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Announcement: The American Union of Crystallography
by Joseph Ferrara 01 Nov '25

01 Nov '25

What is the American Union of Crystallography (AUC)? The American Union of Crystallography (AUC) is a nonprofit scientific and educational organization established in 2025 to represent and support the U.S. crystallographic community at both national and international levels. It was formed in response to the USA National Science Foundation's (NSF) decision not to fund the U.S. National Committee for Crystallography (USNC/Cr). As a result, the National Academy of Sciences (NAS) will cease serving as the U.S. adhering body to the International Union of Crystallography (IUCr), effective January 1, 2026. While NSF will continue to support other national scientific committees directly, it has ended centralized funding through the NAS, necessitating the creation of the AUC as an independent successor. The AUC was officially incorporated in the state of Delaware on April 22, 2024, and received Internal Revenue Service 501(c)(3) nonprofit status on August 21, 2025. On September 4, 2025, the IUCr Executive Committee granted the AUC ad interim adhering body status, effective January 1, 2026, enabling it to represent the USA to the IUCr until the General Assembly in Calgary in 2026. Mission and Core Objectives The AUC serves as the national voice for U.S. crystallographers and is committed to advancing crystallographic science through the following objectives: * Represent U.S. crystallographers to the IUCr. * Advocate strong, sustained support of crystallographic research. * Promote interdisciplinary collaboration to accelerate scientific discovery. * Support education and training for the next generation of crystallographers. * Expand outreach to showcase real-world applications of crystallography. * Steward the USNC/Cr's financial resources responsibly. * Operate as a volunteer-led organization responsive to community needs. * Recognize and celebrate distinguished members of the community. Current Priorities With nonprofit status and international recognition in place, the AUC is focused on the following immediate priorities: * Supporting U.S.-based education and training initiatives, including student travel to the IUCr Congress. * Managing the newly established George M. Sheldrick Award for Contributions to Structural Science. * Contributing to the success of the 2026 IUCr Congress and General Assembly in Canada. * Establishing key committees on Workforce & Education, Finance, Ethics, and other areas as needed. * Managing and growing the legacy funds originally held by NAS to support U.S. crystallography. Governance and Community Engagement To ensure transparency and continuity, all current USNC/Cr members will serve on the AUC Board through 2025. Beginning in 2026, Board members will be selected through an open and inclusive nomination process, with active involvement from the U.S. National Division of the American Crystallographic Association (USND, ACA). The AUC's bylaws are modelled on those of the USNC/Cr, and the organization is committed to continued community input as it grows. Why Not the ACA or USND? The ACA is a regional affiliate representing both U.S. and Canadian crystallographers and is not structured to take on U.S.-specific international responsibilities. The USND, while created as a possible successor to the USNC/Cr, is not a standalone legal entity and therefore cannot function as an independent 501(c)(3) organization. A Call to Action The AUC invites all members of the U.S. crystallographic community to support its leadership, mission, and transition by: * Participating in AUC initiatives through service, collaboration, and advocacy. * Supporting the transfer of NAS-held legacy funds to the AUC for continued stewardship. We ask the worldwide crystallographic community to support the AUC by voting to make it the permanent adhering body representing the US at the General Assembly in Calgary in August 2026. Together, we can ensure a strong, sustainable, and globally connected future for U.S. crystallography. Joseph D. Ferrara, Chair USNC/Cr; President and Chair, AUC Lisa J. Keefe, Vice-Chair USNC/Cr; Vice President and Secretary, AUC Ilia A. Guzei, Secretary-Treasurer USNC/Cr; Treasurer, AUC

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.cif file from phenix for AF3 as template
by Georg Mlynek 29 Oct '25

29 Oct '25

Dear Phenix community, I have solved the structure of protein complex consisting of 6 chains. We have the structure with 5 chains now and still see positive electron density and mass spec analysis gave us some possible candidates which we would like to model with AF3. However just using MSA's AF3 is not placing two chains correctly, therefore I want to give the structure templates for the 5 chains. However using the proposed way to create the files *https://github.com/google-deepmind/alphafold3/issues/462 * I get an error: ValueError: INVALID_ARGUMENT: The number of values (1958407) in a loop is not a multiple of the number of the loop's columns (19) However it works if I use 5Y2E.cif from PDB. Comparing the cif files I see a difference. from phenix: loop_ _atom_site.group_PDB _atom_site.id _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.type_symbol _atom_site.pdbx_formal_charge _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_model_num from 5Y2E loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num After processing 5Y2E loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num Did anybody encountered the same problem and has a workaround? Additionally I would like to ask if anybody knows which entries of the cif file header are really needed for AF3 to run? I would like to make a google colab which does the processing, without relying on the structure module from AF3 code (from alphafold3 import structure). There is a Python Package with the same name "alphafold3" on PyPi but this does not have a structure subpackage. Many thanks, br Georg.

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Importing a project
by jiyeol3＠uci.edu 29 Oct '25

29 Oct '25

Hi, I am trying to import a project, but every time I do it, it does not load the job history. How do I fix this? The original folder contains all the files.

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CBMS Lecture Series - Vanden Zanden
by Stojanoff, Vivian 23 Oct '25

23 Oct '25

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Crystal Vander Zanden University of Colorado www.vanderzanden-lab.com<https://urldefense.com/v3/__http://www.vanderzanden-lab.com/__;!!P4SdNyxKAP…> WEDNESDAY, November 19, 13:30 (EST) "Assessing Membrane Protein Structures Using Liquid Surface X-ray Scattering” Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/2R2GbeNJTa-QtcoJRA7Vjw<https://urldefense.com/v3/__https://bnl.zoomgov.com/meeting/register/2R2Gbe…> Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: In the Vander Zanden lab, we use complementary liquid surface X-ray scattering and molecular dynamics methods to study the structure of protein/membrane interactions, particularly focusing on protein families that have dynamic behavior at membrane surfaces. Specifically, X-ray reflectivity and grazing incidence diffraction will be showcased as powerful tools for determining structural information about peripheral membrane proteins. We will discuss application of these techniques to study three protein/membrane systems: glycolipid recognition proteins, amyloidogenic proteins, and lipoxygenase enzymes. For each of these systems, a lipid monolayer is deposited at the air/water interface in a Langmuir trough, and proteins are injected into the liquid subphase below, where they can bind the membrane. These thin-film measurements are used to deduce an electron density profile describing the membrane and bound proteins. Diffraction data are used to detect semi-ordered species present at the membrane, such as protein assemblies and lipids organized into condensed domains. Overall, we feel these methods are a valuable addition to the classic suite of structural biology techniques, and their strength is the ability to capture a population of membrane proteins exhibiting dynamic behavior. ================= Vivian Stojanoff, PhD Education, Training, Outreach User Program p 1(631) 344 8375 e lifescience(a)bnl.gov<mailto:[email protected]> w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/> Address: Center for Biomolecular Structure National Synchrotron Light Source II Building 745 Brookhaven National Laboratory Upton NY 11973 ________________________________ To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?…>

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Problem when trying to install last nighlty build on Ubuntu 22.04
by emmanuel.bettler＠univ-lyon1.fr 21 Oct '25

21 Oct '25

Hi, on a linux ubuntu 22.04 distribution, when i'm trying to install latest Phenix nightly version 2.0-5824, i have the following error message: [...] PREFIX=/home/ebettler/Soft/phenix-2.0-5824 Unpacking bootstrapper... Unpacking payload... entry_point.py:256: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. entry_point.py:256: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. concurrent.futures.process._RemoteTraceback: ''' Traceback (most recent call last): File "concurrent/futures/process.py", line 432, in wait_result_broken_or_wakeup File "multiprocessing/connection.py", line 251, in recv TypeError: InvalidArchiveError.__init__() missing 1 required positional argument: 'msg' ''' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "entry_point.py", line 244, in _constructor_extract_conda_pkgs File "concurrent/futures/_base.py", line 449, in result File "concurrent/futures/_base.py", line 401, in __get_result concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "entry_point.py", line 691, in <module> File "entry_point.py", line 681, in main File "entry_point.py", line 582, in _constructor_subcommand File "entry_point.py", line 246, in _constructor_extract_conda_pkgs RuntimeError: Failed to extract /home/ebettler/Soft/phenix-2.0-5824/pkgs/chem_data-2.0.5824-pyhe0d8492_0.conda: A process in the process pool was terminated abruptly while the future was running or pending. [PYI-197168:ERROR] Failed to execute script 'entry_point' due to unhandled exception! What's wrong ? Any advice are welcome !

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Off-topic: Postdoc opportunity – Protein–protein interactions / Quantitative Interactomics
by Gergő Gógl 20 Oct '25

20 Oct '25

Dear colleagues, Sorry for the off-topic post, but I would like to share a *postdoctoral position* open in my team at the *Institut de Biologie Valrose (iBV)* in Nice, France. Our group investigates *motif-mediated protein–protein interactions* underlying key biological processes such as *cell signaling* and *cancer*, using *quantitative interactomics* and *biophysical approaches* (e.g. the *native holdup assay*). We are looking for a motivated researcher who has *recently defended their PhD*, with experience in *recombinant protein production and purification*. Expertise in *biochemistry*, *biophysics*, or *structural biology* would be highly relevant, and the position offers opportunities to apply these skills to proteome-wide interaction mapping. *Start date:* as early as December *Contract:* 6 months, with possible extension *Location:* iBV, Nice, France Full details of the call: https://euraxess.ec.europa.eu/jobs/381589 Best regards, *Gergo Gogl* Team *Quantitative Interactomics and Disease-Related Networks* *Institut de Biologie Valrose (iBV), Nice*

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Zero B-factors
by p.auffinger＠unistra.fr 20 Oct '25

20 Oct '25

Hi, I have a large structure for which I just want to update B-factors. Unfortunately, I get zero values for some B-factors. Basically, I modified coordinates of a PDB deposited file and used the deposited cry-EM map. Is there something in the header (present or missing) that could influence the outcome of such a calculation ? Thanks, Pascal

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Structural Biology Full Professorship, University of Innsbruck, Austria
by Bernhard Rupp 18 Oct '25

18 Oct '25

Hi Fellows, a Full Professor position in Structural Biology is open at the Leopold-Franzens University in Innsbruck, Austria. Feel free to contact me about position details and questions, including the origins of the euphemistic title 'Structural Analysis for Pharmacy and Chemistry' in the attached posting. Best regards, BR ------------------------------------------------------ Bernhard Rupp k.k. Hofkristallamt San Diego, CA 92084 https://www.hofkristallamt.org/ https://psilosophy.org/ br(a)hofkristallamt.org +1 925 209 7429 ------------------------------------------------------ Institute of Theoretical Chemistry University Innsbruck Am Innrain 82 A 6020 Innsbruck bernhard.rupp(a)uibk.ac.at +43 676 571 0536 ------------------------------------------------------ Many plausible ideas vanish at the presence of thought ------------------------------------------------------

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Multiple Linux users access same project directory
by André Graça 10 Oct '25

10 Oct '25

Hi everyone, Is there any possibility to set up Phenix so multiple Linux users of the same Linux machine can access the same project directory? Thank you, André

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Generating BIOMT record for icosahedral symmetry
by Lei Chen 06 Oct '25

06 Oct '25

Dear All, I am currently working on depositing a PDB file for an icosahedral virus and have built the pdb for one asymmetric unit (ASU). I am wondering how I can compile or obtain the BIOMT record. I haven't found a detailed protocol online. Thank you, Lei

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