- phenixbb - phenix-online.org

Problem when trying to install last nighlty build on Ubuntu 22.04
by emmanuel.bettler＠univ-lyon1.fr 04 Nov '25

04 Nov '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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Announcement: The American Union of Crystallography
by Joseph Ferrara 31 Oct '25

31 Oct '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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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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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 05 Oct '25

05 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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Generating BIOMT record for icosahedral symmetry
by rainfieldcn 03 Oct '25

03 Oct '25

Dear All, I am currently working on depositing a PDB file for an icosahedral virus and have built the 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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PhD Position – Structural and Functional Studies of Plant Membrane-Protein Transporters, Department of Molecular Biology and Genetics, Aarhus University, Denmark
by Bjørn Panyella Pedersen 02 Oct '25

02 Oct '25

We have an open phd position in our new Plant-PATH center. You will be doing biophysics and structural biology on plant hormone transporters in a great and international team. See details below ________________________________ Dear colleagues, Please pass this along to anyone who might be interested. Thanks! /Bjørn PhD Position – Structural and Functional Studies of Plant Membrane-Protein Transporters, Department of Molecular Biology and Genetics, Aarhus University, Denmark online posting: https://www.linkedin.com/posts/plant-path-center_exciting-phd-opportunity-i… The Opportunity The Plant-PATH Center for Active Transport of Plant Hormones is seeking a motivated PhD student to join Bjørn Panyella Pedersen’s lab. This is a unique chance to study the molecular mechanisms of transmembrane hormone and sugar transport in plants and explore how these processes could contribute to more sustainable agriculture. You will work at the intersection of structural biology, biophysics, and plant physiology, within an international, interdisciplinary team spanning Denmark, Germany, and Belgium. At Plant-PATH, we value team spirit, curiosity, and collaboration, and we are looking for a candidate who will thrive in this environment. About the role The exact focus will be shaped with the successful candidate but will involve structural studies of plant membrane proteins that control growth (cryo-EM, X-ray crystallography), and functional assays linking structure to transport activity (e.g., electrophysiology in oocytes, reconstitution in liposomes). The following recent publications illustrate our work: • Ung et al., Nature Plants (2025): AUX/LAX transporters and auxin import • Schulz et al., Nature Plants (2025): Herbicide transport by PIN-FORMED auxin transporters • Andersen et al., PNAS (2025): Molecular selectivity in STP6 and STP10 sugar transport proteins Who we are looking for The ideal candidate will have… • MSc in biochemistry, molecular biology, or a related field • Hands-on experience with molecular cloning, protein expression, and purification (membrane protein experience a plus) • Curiosity, teamwork spirit, and willingness to ask challenging questions • Some experience with cryo-EM, X-ray data, or transport assays (helpful, but not required) What we offer • Fully funded 3-year PhD with competitive salary • Access to state-of-the-art facilities (Titan Krios, X-ray beamlines, biophysical instruments) • Supportive, collaborative, and interdisciplinary environment, where all ideas are welcomed • Collegial culture valuing equality, work-life balance, and regular social events • The chance to be part of the Plant-PATH Centre of Excellence, funded by the Danish National Research Foundation, providing a collaborative network with frequent exchanges, joint seminars and opportunities to spend time in partner labs in Denmark, Belgium, and Germany • Life in Aarhus: a vibrant, green, and safe international city, with rich café culture, thriving arts scene, and abundant outdoor and water sports How to apply Send your CV, a short motivation letter, and two references to Prof. Bjørn Panyella Pedersen (bpp(a)mbg.au.dk) by 15 October 2025 Questions? Feel free to contact Leila Margot Henkes, Centre Coordinator (lmh(a)mbg.au.dk). -- Bjørn Panyella Pedersen, Professor, PhD Director, DNRF Center for Active Transport of Plant Hormones (Plant-PATH) Dept. of Molecular Biology and Genetics - Aarhus University Tel: +45 2972 3499 | mail: bpp(a)mbg.au.dk | DNRF Center: plant-path.au.dk | Lab: pedersenlab.dk

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inconsistency of Molprobity results between RealSpaceRefine and ValidationCryoEM
by Kevin M Jude 25 Sep '25

25 Sep '25

I notice inconsistencies in the Molprobity results reported for the same structure from RealSpaceRefine and from ValidationCryoEM. As an example, for bond angle restraints, RSR reports that there are four >4sigma outliers (but does not list the outliers), while ValidationCryoEM reports 0. RSR CryoEMValidation Number of restraints 13228 13228 RMS(deviation) 0.509 0.51 Max. deviation 9.997 9.998 Min. deviation 0 0 Number of outliers > 4sigma 4 0 Browsing through the .geo file, I don’t see any >4 sigma deviations among the highest residual angles, so I think this is an error. I also see small discrepancies in Ramachandran favored, rotamer outliers, and clash score which seem to come down to minuscule differences in measurements at the margins. This is for Phenix 1.21.2-5419. Happy to share files offline. -- 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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ensemble refinement with twinned data
by georgep＠rice.edu 24 Sep '25

24 Sep '25

Last version of phenix I checked, one cannot do an ensemble refinement with twin data. Anyone know how to do this? If its not worth fixing, can anyone point to a sample cctbx script to start from? Thanks,

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[Bug report] scitbx.array_family range error when running phenix.elBOW with SMILES input
by zengpei23＠mails.ucas.ac.cn 17 Sep '25

17 Sep '25

Dear Phenix developers, I encountered a reproducible error while trying to generate a ligand CIF file using phenix.elBOW. The program terminates with a scitbx.array_family range error. Below I provide the details. SMILES string:CSCCC(=N)C1=NC(=Cc2ccc(O)cc2)C(=O)N1CC=O Geometry optimisation ： elBOW AM1 Would you please help to diagnose whether this is due to: an internal bug in SMILES parsing/geometry optimisation, or a limitation in handling this specific ligand structure? I can provide the full log file if needed. Thank you for your time and support. Best regards, zeppelin

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PhD Position – Structural and Functional Studies of Plant Membrane-Protein Transporters, Department of Molecular Biology and Genetics, Aarhus University, Denmark
by Bjørn Panyella Pedersen 16 Sep '25

16 Sep '25

Dear colleagues, Please pass this along to anyone who might be interested. Thanks! /Bjørn PhD Position – Structural and Functional Studies of Plant Membrane-Protein Transporters, Department of Molecular Biology and Genetics, Aarhus University, Denmark online posting: https://www.linkedin.com/posts/plant-path-center_exciting-phd-opportunity-i… The Opportunity The Plant-PATH Center for Active Transport of Plant Hormones is seeking a motivated PhD student to join Bjørn Panyella Pedersen’s lab. This is a unique chance to study the molecular mechanisms of transmembrane hormone and sugar transport in plants and explore how these processes could contribute to more sustainable agriculture. You will work at the intersection of structural biology, biophysics, and plant physiology, within an international, interdisciplinary team spanning Denmark, Germany, and Belgium. At Plant-PATH, we value team spirit, curiosity, and collaboration, and we are looking for a candidate who will thrive in this environment. About the role The exact focus will be shaped with the successful candidate but will involve structural studies of plant membrane proteins that control growth (cryo-EM, X-ray crystallography), and functional assays linking structure to transport activity (e.g., electrophysiology in oocytes, reconstitution in liposomes). The following recent publications illustrate our work: • Ung et al., Nature Plants (2025): AUX/LAX transporters and auxin import • Schulz et al., Nature Plants (2025): Herbicide transport by PIN-FORMED auxin transporters • Andersen et al., PNAS (2025): Molecular selectivity in STP6 and STP10 sugar transport proteins Who we are looking for The ideal candidate will have… • MSc in biochemistry, molecular biology, or a related field • Hands-on experience with molecular cloning, protein expression, and purification (membrane protein experience a plus) • Curiosity, teamwork spirit, and willingness to ask challenging questions • Some experience with cryo-EM, X-ray data, or transport assays (helpful, but not required) What we offer • Fully funded 3-year PhD with competitive salary • Access to state-of-the-art facilities (Titan Krios, X-ray beamlines, biophysical instruments) • Supportive, collaborative, and interdisciplinary environment, where all ideas are welcomed • Collegial culture valuing equality, work-life balance, and regular social events • The chance to be part of the Plant-PATH Centre of Excellence, funded by the Danish National Research Foundation, providing a collaborative network with frequent exchanges, joint seminars and opportunities to spend time in partner labs in Denmark, Belgium, and Germany • Life in Aarhus: a vibrant, green, and safe international city, with rich café culture, thriving arts scene, and abundant outdoor and water sports How to apply Send your CV, a short motivation letter, and two references to Prof. Bjørn Panyella Pedersen (bpp(a)mbg.au.dk) by 15 October 2025 Questions? Feel free to contact Leila Margot Henkes, Centre Coordinator (lmh(a)mbg.au.dk). -- Bjørn Panyella Pedersen, Professor, PhD Director, DNRF Center for Active Transport of Plant Hormones (Plant-PATH) Dept. of Molecular Biology and Genetics - Aarhus University Tel: +45 2972 3499 | mail: bpp(a)mbg.au.dk | DNRF Center: plant-path.au.dk<https://plant-path.au.dk/> | Lab: pedersenlab.dk<http://www.pedersenlab.dk> -- Bjørn Panyella Pedersen, Professor, PhD Director, DNRF Center for Active Transport of Plant Hormones (Plant-PATH) Dept. of Molecular Biology and Genetics - Aarhus University Tel: +45 2972 3499 | mail: bpp(a)mbg.au.dk | DNRF Center: plant-path.au.dk<https://plant-path.au.dk/> | Lab: pedersenlab.dk<http://www.pedersenlab.dk>

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adding together
by James Holton 12 Sep '25

12 Sep '25

Greetings Phenix developers! I have what I hope is a quick question. I'm trying to add a stack of phased structure factors together. Specifically from separate runs of phenix.fmodel. Normally, I'd use sftools for this, but the distributed version has a size limitation. According to Tom's phenix chatbot, I can use phenix.maps for adding two sets of structure factors together, but it seems to only want to combine an mtz with a pdb. There is iotbx.reflection_file_editor, but it only works from the GUI (and I want to add 1000 mtz files together). phenix.xmanip looks promising too, but again, seems to want a pdb and an mtz. Is there a recommended way to do this? I've already asked this on CCP4BB, but I wanted to get the Phenix take on these kinds of manipulations. Thank you, -James Holton MAD Scientist

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Re: phenixbb Digest, Vol 237, Issue 1 (out of office)
by Elisabeth Laurent 12 Sep '25

12 Sep '25

Thank you for your e-mail. I am out of office until September 15th, 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> 12.9.25 20:35 >>> 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. atom selection for elements anisotropic rest TLS (Georg Mlynek) 2. Re: atom selection for elements anisotropic rest TLS (John Bacik) 3. adding together (James Holton) 4. Re: adding together (Petrus Zwart) ---------------------------------------------------------------------- Message: 1 Date: Wed, 10 Sep 2025 08:17:54 +0200 From: Georg Mlynek <georg.mlynek(a)univie.ac.at> Subject: [phenixbb] atom selection for elements anisotropic rest TLS To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Message-ID: <676e375c-3d60-438c-adc8-8f6942afb591(a)univie.ac.at> Content-Type: text/plain; charset=UTF-8; format=flowed Dear scientific community, I ticked TLS parameters in Strategy and in Selection Editor I choose 1 group/chain. Then under Anisotropy elements I typed: element Mn or element Mg Running this throws the error: Bad (empty or mixed) selection in adp_individual_iso. What would be the right input under Isotropic atoms so the TLS is not mixed up. Many thanks, br Georg. ------------------------------ Message: 2 Date: Wed, 10 Sep 2025 18:38:38 +0000 (UTC) From: John Bacik <mxjpb(a)yahoo.com> Subject: [phenixbb] Re: atom selection for elements anisotropic rest TLS To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org>, Georg Mlynek <georg.mlynek(a)univie.ac.at> Message-ID: <40790919.1197232.1757529518607(a)mail.yahoo.com> Content-Type: text/plain; charset=UTF-8 Hi Georg, if you are trying to refine anisotropic B-factors for a Mn or Mg element only I do not think you need TLS parameters for that. One way to refine specific elements would be in Refinement settings/Modify start model/B-factors/tick "Convert to anisotropic" and select for the Mn or Mg element. Any element that is formatted as anisotropic will remain so through subsequent rounds of refinement. All the best,John On Wednesday, September 10, 2025 at 01:18:06 AM CDT, Georg Mlynek <georg.mlynek(a)univie.ac.at> wrote: Dear scientific community, I ticked TLS parameters in Strategy and in Selection Editor I choose 1 group/chain. Then under Anisotropy elements I typed: element Mn or element Mg Running this throws the error: Bad (empty or mixed) selection in adp_individual_iso. What would be the right input under Isotropic atoms so the TLS is not mixed up. Many thanks, br Georg. _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org Unsubscribe: phenixbb-leave@%(host_name)s ------------------------------ Message: 3 Date: Fri, 12 Sep 2025 11:28:47 -0700 From: James Holton <jmholton(a)lbl.gov> Subject: [phenixbb] adding together To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Message-ID: <e2697b82-63b6-4b06-addb-f3c583d10851(a)lbl.gov> Content-Type: text/plain; charset=UTF-8; format=flowed Greetings Phenix developers! I have what I hope is a quick question. I'm trying to add a stack of phased structure factors together. Specifically from separate runs of phenix.fmodel. Normally, I'd use sftools for this, but the distributed version has a size limitation. According to Tom's phenix chatbot, I can use phenix.maps for adding two sets of structure factors togetheiotbx.reflection_file_editor, but it only works from the GUI (and I want to add 1000 mtz files together). phenix.xmanip looks promising too, but again, seems to want a pdb and an mtz. Is there a recommended way to do this? I've already asked this on CCP4BB, but I wanted to get the Phenix take on these kinds of manipulations. Thank you, -James Holton MAD Scientist ------------------------------ Message: 4 Date: Fri, 12 Sep 2025 11:34:35 -0700 From: Petrus Zwart <phzwart(a)lbl.gov> Subject: [phenixbb] Re: adding together To: James Holton <jmholton(a)lbl.gov> Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> Message-ID: <CA+_q3A1hONE54pVQJ70H10Y9fskYZL-haw_BrMuZq150a8cG=w(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" https://claude.ai/public/artifacts/f390c669-b8c7-4776-a4bc-1761b110bba0 On Fri, Sep 12, 2025 at 11:29 AM James Holton <jmholton(a)lbl.gov> wrote: > Greetings Phenix developers! > > I have what I hope is a quick question. I'm trying to add a stack of > phased structure factors together. Specifically from separate runs of > phenix.fmodel. Normally, I'd use sftools for this, but the distributed > version has a size limitation. According to Tom's phenix chatbot, I can > use phenix.maps for adding two sets of structure factors together, but > it seems to only want to combine an mtz with a pdb. There is > iotbx.reflection_file_editor, but it only works from the GUI (and I want > to add 1000 mtz files together). phenix.xmanip looks promising too, but > again, seems to want a pdb and an mtz. Is there a recommended way to do > this? > > I've already asked this on CCP4BB, but I wanted to get the Phenix take > on these kinds of manipulations. > > Thank you, > > -James Holton > MAD Scientist > > _______________________________________________ > phenixbb mailing list -- phenixbb(a)phenix-online.org > To unsubscribe send an email to phenixbb-leave(a)phenix-online.org > Unsubscribe: phenixbb-leave@%(host_name)s -- ------------------------------------------------------------------------------------------ Peter Zwart Staff Scientist, Molecular Biophysics and Integrated Bioimaging Berkeley Synchrotron Infrared Structural Biology Biosciences Lead, Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 ------------------------------------------------------------------------------------------ ------------------------------ Subject: Digest Footer _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org ------------------------------ End of phenixbb Digest, Vol 237, Issue 1 ****************************************

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atom selection for elements anisotropic rest TLS
by Georg Mlynek 10 Sep '25

10 Sep '25

Dear scientific community, I ticked TLS parameters in Strategy and in Selection Editor I choose 1 group/chain. Then under Anisotropy elements I typed: element Mn or element Mg Running this throws the error: Bad (empty or mixed) selection in adp_individual_iso. What would be the right input under Isotropic atoms so the TLS is not mixed up. Many thanks, br Georg.

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help with circular peptide cif file creation
by John Bruning 07 Sep '25

07 Sep '25

Dear Phenix BB, We have a 15 aa circular peptide. It has numerous non-natural amino acids, including 1-2 that aren't in the PDB anywhere. Where have created a cif file that allows Phenix refine to run without craching, but I am not sure I am doing it right, and it was kind of complicated. I was wondering if there was anyone out there with ample experience with this type of thing that could help us check over our cif and more importantly recommend the best way to make these cif files in the future. Thanks, Dr. John B. Bruning Head, Laboratory of Protein Crystallography and Structural Biology Associate Professor Oracle For Research Fellow Institute of Photonics and Advanced Sensing School of Biological Sciences, Discipline of Molecular and Biomedical Science Faculty of Sciences, Engineering and Technology The University of Adelaide Adelaide, South Australia 5005 Telephone: +61 08 8313 5218 Email address: john.bruning(a)adelaide.edu.au<mailto:[email protected]>

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Postdoctoral Position – Computational Methods for Cryo-EM at LBNL
by Pavel Afonine 03 Sep '25

03 Sep '25

Dear community, Posting on behalf of Kanupriya Pande: I’d like to draw your attention to the following job opening at Lawrence Berkeley National Laboratory (California, USA): We are looking for a postdoctoral candidate at Lawrence Berkeley Lab (California, US) to work on an exciting project on computational methods development for cryo-electron microscopy. The project is on developing mathematical approaches and computational algorithms to investigate protein conformational states from cryo-EM experiments, including single-particle imaging and cellular tomography. Goals include developing a pipeline for automated atomic modeling of heterogeneous structures from cryo-EM data using Phenix model building tools and developing methods for dealing with preferred orientation, incomplete data and structure completion. You will work with a data analysis team for image analysis and the Phenix team for model building aspects. The position can start as early as Oct 1, 2025. Full details of the position and job requirements can be found here: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-cryo-em-7131 Please feel free to share this opportunity with anyone who might be interested. Kind regards, Pavel

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partial structure refinement
by James Holton 02 Sep '25

02 Sep '25

Greetings PhenixBB, I have a question that keeps coming up again and again. If I have a part of my structure that is a blob of density and I have a map of what that density cloud looks like, is there any way in phenix to include that blob as part of the refinement? Perhaps giving it its own scale and B factor? One example might be a user-defined bulk solvent map, but a disordered ligand or domain can also come up. Traditionally, in older refinement programs this was called a "partial structure", and it is a feature still supported in refmac5. You give it "FPART=F PHIP=P" in the input mtz file. Last I checked there was no way to do this in phenix. Is that still true? Any recommended ways to do things like this? Thanks for your help and insight, -James Holton MAD Scientist

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Pittsburgh Diffraction Conference 2025 - Pre Conference Workshop - Last Days to register
by Stojanoff, Vivian 26 Aug '25

26 Aug '25

Pittsburgh Diffraction Conference You are cordially invited to attend the Pre-Conference Workshop, Crystal Clear Insights: Mastering Protein Crystallization (for the future) LAST DAYS for REGISTRATION AUGUST 29, (Friday 2025 This hands-on workshop will be held at NSLS II on October 9 prior to the Pittsburgh Diffraction Conference. “Crystal Clear Insights” introduces crystallizations methods for the upcoming X-ray sources (time resolved, room temperature, serial crystallography), electron microscopy and neutron diffraction. REGISTRATION by August 29, 2025, in the Brookhaven National Laboratory Guest, User and Visitor Center (GUV), if you do not have a valid BNL Guest appointment. To register follow instructions: https://guest.bnl.gov/ Contact: Vivian Stojanoff by email (stojanof(a)bnl.gov) and use “PDC 2025 – Crystal Clear” for your subject line Program: Lecture: From Gene to Crystallization Crissy Tarver, SLAC Hand-on Topics: Exploring the Phase Diagram for crystals for all applications Patrick Stewart, Douglas Instruments Ltd. Nanoliter and nano/micro sized crystals using the Acoustic Droplet Ejector Alex Soares, NSLS II Microfluidics crystallization and X-ray Diffraction Sarah Perry, UMASS Amherst Vapor Diffusion Methods Darya Marchany-Rivera, SSRL Sample prep for electron microscopy and X-ray diffraction Joyce Frank (Mitegen) & Crissy Tarver (SLAC)

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CBMS invites - PDC2025 workshop Crystal Clear Insights - Deadline August 29
by Stojanoff, Vivian 22 Aug '25

22 Aug '25

The Center for Biomolecular Structure invites you to participate in the 82th Pittsburgh Diffraction Conference (PDC) PDC 2025 - Pre Conference hands-on workshop: Crystal Clear Insights: Mastering Protein Crystallization registration deadline AUGUST 29. This workshop guides you through cutting-edge crystallization strategies tailored to X-ray, electron, or neutron diffraction. You will explore the latest approaches for producing microcrystals for serial experiments, designing crystallization pipelines for fragment screening, optimizing conditions for time-resolved crystallography. Alongside the core methods, we’ll highlight practical tips and tricks drawn from current practice: from seeding strategies and microcrystal preparation to cryoprotection, and sample delivery. To register please follow instructions provided: https://www.bnl.gov/pittsburgh-diffraction-conference/reg/step1.php ALL participants need to register as well in the Guest, User and Visitor Center as this workshop will take place at the National Synchrotron Light Source II https://guest.bnl.gov/ ON THE PROGRAM : Lecture: From genes to structure - Crissy Tarver (SLAC) Hands-on * Learn tricks and tips: from hanging drops to sitting drops in vapor diffusion methods Darya Marchany-Rivera (SLAC) * Explore the Phase Diagram for crystals for all applications ; Patrick Shaw Stewart (Douglas Instruments Ltd.) * Learn about nanoliter and nano/micro-sized crystals using the Acoustic Dropplet Ejector; Alex Soares (NSLS II) * Discover microfluidics crystallization and X-ray diffraction; Sarah Perry (University of Massachusetts Amherst) * From crystals to cryo EM samples: what they have in common; Joyce Frank (Mitegen LLC) & Crissy Tarver (SLAC) For accommodations we suggest HomeSuites2by Hilton Long Island Brookhaven (https://www.hilton.com/en/locations/usa/new-york/yaphank/home2-suites/), and Springhill Suites by Marriott Long Island Brookhaven (https://www.marriott.com/en-us/hotels/ispsh-springhill-suites-long-island-b…) ask for discount for longer stay.

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Pacific Northwest CryoEM Center Modelling Workshop
by Davulcu, Omar 21 Aug '25

21 Aug '25

Dear all, The Pacific Northwest CryoEM Center is excited to announce that registration is open for our first Atomic Modelling and Validation in CryoEM workshop! This virtual workshop is open to all and will explore current methods, best practices, and potential pitfalls of atomic modelling in cryoEM. Join us on September 3 - 5 to hear software developers and end users discuss state-of-the-art modelling tools and their applications. Registration is required and free and open to all. Please see the attached flyer to learn more and visit http://tinyurl.com/Cryo-EMModeling to register! Best, Omar Davulcu Scientific Point of Contact Pacific Northwest Cryo-EM Center http://pncc.labworks.org<http://pncc.labworks.org/>

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Reminder: CBMS Lecture Series - daSilva - August 20, 13:30 (EDT)
by Stojanoff, Vivian 19 Aug '25

19 Aug '25

You and your co-workers are cordially invited to join us ..... "AI Tools in X-ray Computed Tomography: Applications, Drawbacks, and Key Insights." Julio-Cesar da Silva CNRS NÉEL Institute Grenoble, France August 20, 13:30(EDT) To register for virtual attendance: https://bnl.zoomgov.com/meeting/register/haKdzCvnReWMVziXnFXMZw Abstract: I will present the most commonly used AI tools in X-ray computed tomography, highlighting their potential drawbacks. Moreover, I will discuss the basic machine learning concepts essential for effectively utilizing these tools and their implementation at the Hub AI for Tomography, AIAX, located in Grenoble, France. After examining densely connected neural networks, convolutional neural networks, and encoder-decoder architectures, I will provide a brief explanation of how the U-Net, MSDNet, Noise2Noise, TomoGAN, and GANRec networks function within the field of tomography. Their primary applications focus on image denoising and 3D image segmentation. The examples provided will be sourced from hard X-ray tomography applied to both biological and materials science specimens. The key takeaway from this presentation is that while AI-generated results can be advantageous, they need to be critically evaluated, as they always require human involvement for refinement. ================= 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

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