- phenixbb - phenix-online.org

REMINDER – Abstract Submission - 2026 ISMSM || DEADLINE - December 15
by Jose Artur Brito 11 Dec '25

11 Dec '25

Dear Colleagues, This is a reminder that abstract submission for the 7th International Symposium on Microbial Sulfur Metabolism (7th ISMSM), will CLOSE in December 15th. The meeting will take place in Lisbon, Portugal, from 17–20 March, 2026, and will bring together researchers from across the globe to explore the latest advances in microbial sulfur cycling, from molecular mechanisms to ecological, environmental and health perspectives. A number of talks will be selected from the abstracts, so please register and submit your abstract! https://wmsm.itqb.unl.pt/registration/ 👉 For more information visit: https://wmsm.itqb.unl.pt/ Please share this announcement with colleagues and collaborators who may be interested. We look forward to welcoming you in Lisbon next March! The Organising Committee Inês Cardoso Pereira, Filipa Sousa, José Artur Brito, Andreia Pimenta and Américo Duarte ismsm(a)itqb.unl.pt --

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Phenix density modification - EMDB deposition
by Dmitry Semchonok 20 Nov '25

20 Nov '25

Dear Colleagues, I am preparing to deposit a cryo-EM structure to EMDB/PDB and have encountered an important question regarding resolution reporting and half-map deposition after Phenix density modification. My Situation: 1. I performed 3D refinement in CryoSPARC, generating two independent half-maps 2. I calculated FSC between these original half-maps at the 0.143 threshold: X Å resolution. 3. I processed these half-maps through Phenix resolve_cryo_em for density modification 4. Phenix reports improved resolution of Y Å (based on corrected FSC as documented in your resolve_cryo_em guide) 5. I generated the corresponding FSC XML file from Phenix showing Y Å Questions: When I deposit to EMDB, I understand the policy requires depositing the original, unmodified half-maps (unfiltered, unmasked, unsharpened). However, when EMDB validates the deposition by independently recalculating FSC from these half-maps, they will obtain X Å, not Y Å. This creates an apparent contradiction: • Deposited FSC XML file: Y Å (from Phenix) • EMDB independent FSC calculation from deposited half-maps: X Å (from originals) * When you apply corrections for correlations introduced by density modification in resolve_cryo_em, does this mean the Y Å resolution should be reported as the official resolution, even though the original half-maps show X Å? * What is the recommended workflow when depositing density-modified maps to ensure consistency and avoid validation conflicts? Additionally: • No atomic model was used; only sequence information • The density modification improved map quality and interpretability as intended Thank you. Kind regards, Dmitry

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path errors phenix 1.21.2-5419 MacOS
by Guenter Fritz 18 Nov '25

18 Nov '25

Dear Phenix developers, I spotted two little errors in the path when phenix_ready_set or phenix.elbow calling files (I fixed it myself by copying the files/folder to the right place) Just for the notes: phenix.ready_set ....... Reduce warnings ERROR CTab(/opt/phenix-1.21.2-5419/lib/python3.9/site-packages/*elbow*/resources/monomer_het_dict.txt): could not open The path should be /opt/phenix-1.21.2-5419/lib/python3.9/site-packages/resources ------------------------------------------ phenix.elbow ....... AssertionError: Missing the file /opt/phenix-1.21.2-5419/lib/python3.9/site-packages/elbow/*elbow*/smiles Path should be /opt/phenix-1.21.2-5419/lib/python3.9/site-packages/elbow/smiles Best regards, Guenter

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RapiData at SSRL 2024
by Smith, Clyde 18 Nov '25

18 Nov '25

Hi everyone, Applications are now open for the 2024 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from April 29 to May 4, 2024. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering) Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2024/ and use the links on the "Application and Registration" page to apply for the course. The application deadline is January 31, 2024. Successful applicants will be notified early in February 2024 and invited to register and book accommodation at SLAC Stanford Guesthouse at that time. A limited amount of support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

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Coot 1 - "Open in Coot" within Phenix - auto loading PDB/mtz/extensions
by kelvin.lau＠epfl.ch 07 Nov '25

07 Nov '25

Hi all As the stability of Coot1 increases I am looking to start the transition there from old Coot I can get Phenix to open Coot 1 via the Open in Coot buttons. However, it does not autoload the PDB/mtz/Phenix extensions. I know there are many differences between Coot 0.9X and Coot1 under the hood so just want to see if this was currently possible or if it’s something due to my parameter setups somewhere. Would be very useful to implement if not. Best Kelvin

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phenix 1.22 based on python 3.9 for Mac ARM
by Roberto Battistutta 06 Nov '25

06 Nov '25

Dear All, does an official versione of phenix 1.22 based on python 3.9 for Mac ARM (M2/M3) exist? I can’t find it in the download page. Or will it come out soon? Thank you. Regards, 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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CAHRA 2025: Announcing the 2025 Community-wide Assessment of cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA)
by Tom Burnley - STFC UKRI 05 Nov '25

05 Nov '25

Dear all, We are pleased to announce the 2025 Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA). Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling high-resolution visualization of dynamic biomolecular assemblies. However, a central challenge remains: developing robust computational methods to model different forms of structural heterogeneity—including continuous motions, discrete states, and compositional variations and to accurately estimate population distributions. To encourage the development and benchmarking of heterogeneous reconstruction algorithms and workflows, we invite the cryo-EM community to analyze three new curated experimental and synthetic datasets: 1. Compositional Heterogeneity 2. Conformational Heterogeneity 3. Pose Entanglement Please join us for a webinar where we will introduce this year's challenge: Friday, November 14 12:00 PM Eastern (US, Canada) / 5:00 PM GMT (UK) Registration: ukri.zoom.us/webinar/register/WN_-G-7jbX_Q26o7Q8DiVCcQg<http://ukri.zoom.us/webinar/register/WN_-G-7jbX_Q26o7Q8DiVCcQg> For all challenge information, datasets, and submission timeline, please visit: heterogeneity.notion.site/challenge<http://heterogeneity.notion.site/challenge> Submissions close on June 1, 2026. Please share this with others who may be interested. We hope you’ll join us for this year’s challenge! The CAHRA Team from the Flatiron Institute, CCP-EM/STFC, and Princeton University

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.cif file from phenix for AF3 as template
by Georg Mlynek 04 Nov '25

04 Nov '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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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 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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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 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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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 08 Sep '25

08 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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PDC 2025 > PRE-Conference: Pittsburgh Diffraction Conference - registration deadline August 25,2025
by Stojanoff, Vivian 14 Aug '25

14 Aug '25

Pittsburgh Diffraction Conference You are cordially invited to attend the Pre-Conference Workshop, Crystal Clear Insights: Mastering Protein Crystallization This hands-on workshop will be held at NSLS II on October 9 prior to the Pittsburgh Diffraction Conference. “Crystal Clear Insights” aims to discuss basic and advance protein crystallization methods for advanced structural diffraction data collection. Participants will be able to select three of the five parallel hands-on sessions. To register: https://www.bnl.gov/pittsburgh-diffraction-conference/index.php If you want to register only for the workshop contact Vivian Stojanoff by email (stojanof(a)bnl.gov) and use “PDC 2025 – Crystal Clear” for your subject line. Participation is limited to 20 participants; those who wish to attend only the pre-Conference workshop will be placed on a waiting list and informed by August 26, 2025. ALL “Crystal Clear” pre-Conference PARTICIPANTS need to register until August 25, 2025, in the Brookhaven National Laboratory Guest, User and Visitor Center (GUV), as well, if you do not have a BNL Guest appointment. To register follow instructions: https://guest.bnl.gov/ If you have any question, contact: stojanof(a)bnl.gov. Tentative Program: Lecture: From Gene to Crystallization Crissy Tarver, SLAC Hand-on Topics: Vapor Diffusion Methods - from hanging drops to sitting drops Darya Marchany-Rivera, SSRL 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 Sample prep for electron microscopy and X-ray diffraction TBD All topics will be offered in parallel, participants will be able to choose 3 topics and rotate through them.

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Inquiry on RMS Value in Phenix PredictAndBuild MR Output
by zx2020＠connect.hku.hk 12 Aug '25

12 Aug '25

Dear All, I hope this email finds you well. While reviewing the MR-related output files generated by Phenix PredictAndBuild (see attached screenshot), I noticed that an RMS value is set in the Phaser input section. I found that in certain cases this parameter can have a significant impact on MR results. Could you kindly advise how this RMS value is determined or calculated within Phenix PredictAndBuild? [??????] Thank you very much for your time and guidance. Best regards, Xin Zhang School of Biomedical Sciences, The University of Hong Kong

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Refine pixel size for EM map?
by Oliver Clarke 01 Aug '25

01 Aug '25

Hi, I remember asking about this some time ago, but I am not sure if it was ever implemented. Is there a way to refine just pixel size for an EM map in phenix.real_space refine (or another phenix utility)? Even just automatically rigid-body fitting a crystal structure and calculating the pixel size with max correlation would be handy. We do this at the moment using Chimera/ChimeraX, but an automated way to do it in phenix would be handy. In the absence of a crystal structure, I wonder if directly refining pixel size during real space refinement would be possible/reasonable at higher resolution (<2Å)? Cheers Oli

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Phenix LigandFit RSCC calculation questions
by Theo Teng 29 Jul '25

29 Jul '25

Dear Phenix developers, I hope this message finds you well. We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit: 1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive? 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? We aim to compare the placements from LigandFit to other ligand placement methods, and your response would be appreciated. Best regards, -- *Theodore W. Teng* Harvard College | Class of 2027 A.B. student in Chemical and Physical Biology Secondary in Global Health and Health Policy

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Re: phenixbb Digest, Vol 235, Issue 4 (out of office)
by Elisabeth Laurent 29 Jul '25

29 Jul '25

Thank you for your e-mail. I am out of office until August 26th, 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> 29.7.25 20:38 >>> 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: Structure with high clashscore (sazanov(a)ist.ac.at) 2. Re: Structure with high clashscore (Pavel Afonine) 3. Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025 (Paul Adams) 4. Phenix LigandFit RSCC calculation questions (Theo Teng) 5. Re: Phenix LigandFit RSCC calculation questions (Bernhard Rupp) ---------------------------------------------------------------------- Message: 1 Date: Tue, 22 Jul 2025 15:09:07 -0000 From: sazanov(a)ist.ac.at Subject: [phenixbb] Re: Structure with high clashscore To: phenixbb(a)phenix-online.org Message-ID: <175319694772.2856041.9789770720208691588(a)cci3.lbl.gov> Content-Type: text/plain; charset="utf-8" Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere). Best Leonid JEROME JOHNSON wrote: > Hello all, > > I'm happy to join the forum! I have a problem with clashscores and would be > grateful for support. > > I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved > to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand > commonly results in high clashscore values) and after numerous rounds of > refinement, the clashscore remains high at 11. I recently tried using > gromacs to energy minimize and got values of 5 and 3 (according to > molprobity), but after refinement these values immediately jumped back up > to ~30. > > I wondered if you could describe the best way to reduce these? > > Attached is my latest round of refinement should you wish to take a look! > > Best, > Jerome ------------------------------ Message: 2 Date: Tue, 22 Jul 2025 10:29:20 -0500 From: Pavel Afonine <pafonine(a)lbl.gov> Subject: [phenixbb] Re: Structure with high clashscore To: phenixbb(a)phenix-online.org, jjohnson19(a)ku.edu.tr Message-ID: <b4b4a347-1f89-44a4-b61b-dac1d2344d24(a)lbl.gov> Content-Type: text/plain; charset=UTF-8; format=flowed Hi All, > Hi, one more possibility - we find that if the structure is refined without hydrogens, but one or more ligands do have hydrogens (not intentionally), then Molprobity adds hydrogens to all residues and clashscore calculated by it (now including hydrogens) jumps a lot. The remedy would be to delete all hydrogens from the structure before the refinement (or refine with hydrogens added everywhere). this is an interesting observation. MolProbity always adds all H to compute clashscore -- one can't compute clashscore without H present. I suspect having H on ligands only triggers it to 'think' that H are already present, and it computes clashscore without adding H to everything else. Could you please send me the file off list (the one that has H only on the ligand)? I think we better investigate this.. >> I'm happy to join the forum! I have a problem with clashscores and would be >> grateful for support. >> >> I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved >> to 2.7 Angstroms. For MD, >> commonly results in high clashscore values) and after numerous rounds of >> refinement, the clashscore remains high at 11. 11 looks just fine. Note, clashscore=0 is not the goal because clashscore does not account for non-standard links and for example, can count as a severe clash atoms involved into nonstandard links, and similar. In Phenix Comprehensive Validation, go over the table of clashes, they are sorted, worst first, and check and try to address top few worst offenders. Pavel ------------------------------ Message: 3 Date: Tue, 22 Jul 2025 10:52:38 -0700 From: Paul Adams <pdadams(a)lbl.gov> Subject: [phenixbb] Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025 To: phenixbb(a)phenix-online.org, CCP4BB(a)jiscmail.ac.uk Message-ID: <616BD923-8C42-4BFA-BCAF-4B7E60F4AC9C(a)lbl.gov> Content-Type: text/plain; charset=utf-8 Dear Colleagues, For those of you that may have missed the deadline, the application deadline has been extended to August 1st. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow this link to the course web site: https://meetings.cshl.edu/courses.aspx?course=C-CRYS In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Most applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] -- ------------------------------ Message: 4 Date: Tue, 29 Jul 2025 14:34:52 -0400 From: Theo Teng <theodoreteng(a)college.harvard.edu> Subject: [phenixbb] Phenix LigandFit RSCC calculation questions To: phenixbb(a)phenix-online.org Message-ID: <CAE39kgR2K4FxFye6YJKO9uWnwQECYhg2+AB=_vRb=NLkw9ToXA(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear Phenix developers, I hope this message finds you well. We had two specific questions about how the real-space correlation coefficient (RSCC) is computed when using Phenix.LigandFit: 1. What radius is used around the ligand or search center when calculating the RSCC during ligand fitting? Is this radius fixed or adaptive? 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? We aim to compare the placements from Lig-- *Theodore W. Teng* Harvard College | Class of 2027 A.B. student in Chemical and Physical Biology Secondary in Global Health and Health Policy ------------------------------ Message: 5 Date: Tue, 29 Jul 2025 11:38:27 -0700 From: Bernhard Rupp <br(a)hofkristallamt.org> Subject: [phenixbb] Re: Phenix LigandFit RSCC calculation questions To: Theo Teng <theodoreteng(a)college.harvard.edu> Cc: phenixbb(a)phenix-online.org Message-ID: <CAA3s99dcrE3j8VRJ6cH__7jv9y1a-ve2sxWcRws3UtsKsUdmag(a)mail.gmail.com> Content-Type: text/plain; charset="UTF-8" There is a modified quote from a famous statistician, which one might keep in mind on such ventures: All ligands are wrong, but some are useful. Cheers, BR ------------------------------------------------------ Bernhard Rupp https://www.hofkristallamt.org/ br(a)hofkristallamt.org br(a)ruppweb.org +1 925 209 7429 +43 676 571 0536 ------------------------------------------------------ People can be divided into three classes: The few who make things happen; The many who watch what is happening; and the overwhelming majority who have no clue what is happening. ------------------------------------------------------ On Tue, Jul 29, 2025 at 11:35 AM Theo Teng <theodoreteng(a)college.harvard.edu> wrote: > Dear Phenix developers, > > I hope this message finds you well. > > We had two specific questions about how the real-space correlation > coefficient (RSCC) is computed when using Phenix.LigandFit: > > 1. What radius is used around the ligand or search center when calculating > the RSCC during ligand fitting? Is this radius fixed or adaptive? > > 2. Which CCTBX function(s) underlie the RSCC calculation used in LigandFit? > > We aim to compare the placements from LigandFit to other ligand placement > methods, and your response would be appreciated. > > Best regards, > -- > > *Theodore W. Teng* > Harvard College | Class of 2027 > A.B. student in Chemical and Physical Biology > Secondary in Global Health and Health Policy > _______________________________________________ > 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 > ------------------------------ 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 235, Issue 4 ****************************************

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Deadline Extended: Macromolecular Crystallography - CSHL Course October 2025
by Paul Adams 22 Jul '25

22 Jul '25

Dear Colleagues, For those of you that may have missed the deadline, the application deadline has been extended to August 1st. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow this link to the course web site: https://meetings.cshl.edu/courses.aspx?course=C-CRYS In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Most applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Structure with high clashscore
by JEROME JOHNSON 22 Jul '25

22 Jul '25

Hello all, I'm happy to join the forum! I have a problem with clashscores and would be grateful for support. I have diffraction data for a 3HP-CoA Synthetase from N. maritimus resolved to 2.7 Angstroms. For MD, I used an alphafold structure (as I understand commonly results in high clashscore values) and after numerous rounds of refinement, the clashscore remains high at 11. I recently tried using gromacs to energy minimize and got values of 5 and 3 (according to molprobity), but after refinement these values immediately jumped back up to ~30. I wondered if you could describe the best way to reduce these? Attached is my latest round of refinement should you wish to take a look! Best, Jerome

4 3

Syntax help: phenix.pdb_tools to remove selected bases from file
by Vorländer,Matthias Kopano 21 Jul '25

21 Jul '25

Hi everyone, I am trying to truncate an RNA chain to backbone only using phenix.pdb tools with this command: phenix.pdbtools input.cif remove="(chain IN and not (phosphate or ribose)" I get: AtomSelectionError: RuntimeError: Atom selection syntax error at word "phosphate". Atom selection string leading to error: (chain IN and not (phosphate or ribose) Based on https://phenix-online.org/documentation/reference/atom_selections.html<https://phenix-online.org/documentation/reference/atom_selections.htmlI> I thought “phosphate” and “ribose” should be valid selection key words, but can’t figure out what I am doing wrong and would appreciate your help : ) Thanks in advance and best wishes, Matthias

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smaller cell volume for accommodating protein complex & no MR solution even very similar template
by 陈成 11 Jul '25

11 Jul '25

Dear PHENIXBB people, I have been working on several data sets collected from crystals grown in co-crystallization trials containing a small molecule and Calprotectin, a heterologous protein dimer comprised of two polypeptides with around 90 and 120 amino acids respectively. The crystallographic structure of Calprotectin complexed with a 18-aa peptide have been deposited in RCSB database under PDB entry 7QUV, with cell parameters a = b = 50.8, c = 148.8 in the P 32 2 1 space group. On the contrast, the bunches of data sets I collected give cell parameters a = b = 38.3, c = 196.3 in the P 6 2 2 space group when an oscilliation angle of 0.5 degree was used or cell parameters a = b = 38.2, c = 149.0 in the P 6 2 2 space group when an oscilliation angle of 0.2 degree was used. In either cases, Matthews_coef analysis would suggest that the crystal cell cannot accommodate the whole Calprotectin complex. I had used each single protein of Calprotectin as the search template for MR, but failed as well. Though Phenix.xtriage suggest nothing wrong with the data sets, however, considering that the two polypeptide conprising Calprotectin is structurally similar, I had also tried indexing the data sets under space group spanning P2, P3 apart from P622 and then run MR by a thorough combination of each data sets and different template choices, which, in opposition to what was expected, still gave no reliable MR solution. It's noteworthy that the diffraction pattern of my crytals seemingly showed that multi-crystal problem or other intrinsic growth defects might be underconsidered. In fact, I've been encountering the above crystallographic situation for 3 times recently, which all bear the following characteristics: (1) cell volume is far smaller than expected for containing targeted macromolecules (protein/DNA) that is used for crystallization. (2) no MR solution is achieved though MR template is extremely and sometimes 100% similar. (3) growth defects such as multi-crystal or fibrous diffraction problems possibly exist. Hopefully someone may have dealt with such issues before. Any suggestions is welcomed! Sincerely Chen PS: This message is also posted on CCP4BB. Cheng Chen, Associate ProfessorSchool of Life Sciences, Building 15, Tianjin University No.92 Weijin Road, Nankai District, Tianjin 300072, China

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Re: phenixbb Digest, Vol 234, Issue 7 (out of office)
by Elisabeth Laurent 01 Jul '25

01 Jul '25

Thank you for your e-mail. I am out of office until July 8th, 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> 1.7.25 21:16 >>> 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: phenix install/splash screen issue (Hekstra, Doeke Romke) 2. Data uncertainty: Minimising it and characterising the uncertainty that remains (John R Helliwell) 3. Postdoc Position - Berkeley, California (Paul Adams) ---------------------------------------------------------------------- Message: 1 Date: Sun, 15 Jun 2025 16:51:46 +0000 From: "Hekstra, Doeke Romke" <doeke_hekstra(a)harvard.edu> Subject: [phenixbb] Re: phenix install/splash screen issue To: Billy Poon <BKPoon(a)lbl.gov> Cc: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Message-ID: <BL0PR07MB38897932A0F5134154C3D9199771A(a)BL0PR07MB3889.nam prd07.prod.outlook.com> Content-Type: text/plain; charset="utf-8" Awesome. Will try later this week! -----Original Message----- From: Billy Poon <BKPoon(a)lbl.gov> Sent: Sunday, June 15, 2025 12:36 PM Cc: phenixbb(a)phenix-online.org Subject: [phenixbb] Re: phenix install/splash screen issue Hi Doeke, I got the GUI to work over VNC using ThinLinc at NERSC. The check used to work in Python 2 because comparing against None was allowed. I updated the code to skip the check if any value is None since it's not so crucial. I'll make another build available tomorrow. Let us know if you find any other issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org On Sat, Jun 14, 2025 at 2:51 PM Hekstra, Doeke Romke < doeke_hekstra(a)harvard.edu> wrote: > Hi Billy, > > Correct, I’m using a remote desktop (open on demand, via vnc). > > Doeke > > Get Outlook for iOS <https://aka.ms/o0ukef> > ------------------------------ > *From:* Billy Poon <BKPoon(a)lbl.gov> > *Sent:* Saturday, June 14, 2025 12:19:00 AM > *To:* Hekstra, Doeke Romke <doeke_hekstra(a)harvard.edu> > *Cc:* phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > *Subject:* Re: [phenixbb] phenix install/splash screen issue > > Hi Doeke, > > Are you running over X or via a virtual desktop? I just tested over X > and the GUI shows up. I'm going to try a remote desktop next. > > The issue is that the GUI is unable to calculate some limit for > placing windows. > > -- > Billy K. Poon > Research Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Fax: (510) 486-5909 > Web: https://phenix-online.org > <https://urldefense.proofpoint.com/v2/url?u=https-3A__phenix-2Donline. > org&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMK > OIsdAAHocfxcg&m=E0acsYpZgOQ4jSQxX3QvM2W7a5egZssjBf25gnnV1q4CSsCigsm5eu > QXFzvdyEen&s=sNVrQKJJi4zo2EFXfPjtPYUxQ_hTsSQ0TT8vAPzd5Lg&e=> > > > On Sat, Jun 14, 2025 at 5:12 AM Hekstra, Doeke Romke < > doeke_hekstra(a)harvard.edu> wrote: > > Hi, > After an ostensibly error-free installation of phenix-2.0-5716 on > linux within an HPC environment, when starting the Phenix GUI, I get > the following error: > > [dhekstra@holygpu7c26105 phenix]$ phenix Error in sys.excepthook: > Traceback (most recent call last): > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py"> Error.show_exception_dialog(type, value, traceback) > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/Err > or.py", > line 76, in show_exception_dialog > if (app.bug_timer.IsRunning() is False): > AttributeError: 'PhenixApp' object has no attribute 'bug_timer' > > Original exception was: > Traceback (most recent call last): > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 136, in OnInit > self.start_gui() > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 151, in start_gui > self.get_screen_params() > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 263, in get_screen_params > self.set_window_height(self.prefs.get_root().gui.max_dialog_height) > File > "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App > .py", > line 266, in set_window_height > if (max_height < self.screen_height) : > TypeError: '<' not supported between instances of 'NoneType' and 'int' > OnInit returned false, exiting... > > ==== > The same error occurred with phenix-2.0-5716 (both using the > Linux-x86_64 installer). > > Could you please advise? > > Thanks, > Doeke > _______________________________________________ > 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 > > _______________________________________________ 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: 2 Date: Mon, 30 Jun 2025 12:34:53 +0100 From: John R Helliwell <jrhelliwell(a)gmail.com> Subject: [phenixbb] Data uncertainty: Minimising it and characterising the uncertainty that remains To: CCP4BB(a)jiscmail.ac.uk, PHENIX user mailing list <phenixbb(a)phenix-online.org> Message-ID: <A26415F8-B11F-463A-B03F-F198BCAAA1AA(a)gmail.com> Content-Type: text/plain; charset=utf-8 Dear Colleagues, I imagine you will be interested in my post at the IUCr Committee on Data Public Forum on this topic of data uncertainty:- https://forums.iucr.org/viewtopic.php?f=39&t=6464&sid=7966a823f22e445ad1a3c… All best wishes, John -- Professor John R Helliwell DSc ------------------------------ Message: 3 Date: Tue, 1 Jul 2025 12:15:56 -0700 From: Paul Adams <pdadams(a)lbl.gov> Subject: [phenixbb] Postdoc Position - Berkeley, California To: phenixbb(a)phenix-online.org, CCP4BB(a)jiscmail.ac.uk Message-ID: <19D7DA5E-15B5-4705-A591-4F28C2F4AC9B(a)lbl.gov> Content-Type: text/plain; charset=us-ascii Dear Colleagues, We are looking for a postdoctoral candidate at Lawrence Berkeley Lab (California, US) to work on an exciting project developing computational methods for cryo-electron microscopy. You will develop 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 incomplete data and structure completion. You will work with a data analysis team for image analysis and the Phenix team for model building methods. You can start as early as August 1, 2025. Full details of the position, description of job requirements are in this link: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-cryo-em-7131 Feel free to pass on to anyone you think might be interested. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice PresidenPrincipal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] -- ------------------------------ 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 234, Issue 7 ****************************************

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Postdoc Position - Berkeley, California
by Paul Adams 01 Jul '25

01 Jul '25

Dear Colleagues, We are looking for a postdoctoral candidate at Lawrence Berkeley Lab (California, US) to work on an exciting project developing computational methods for cryo-electron microscopy. You will develop 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 incomplete data and structure completion. You will work with a data analysis team for image analysis and the Phenix team for model building methods. You can start as early as August 1, 2025. Full details of the position, description of job requirements are in this link: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-cryo-em-7131 Feel free to pass on to anyone you think might be interested. Cheers, Paul -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Data uncertainty: Minimising it and characterising the uncertainty that remains
by John R Helliwell 30 Jun '25

30 Jun '25

Dear Colleagues, I imagine you will be interested in my post at the IUCr Committee on Data Public Forum on this topic of data uncertainty:- https://forums.iucr.org/viewtopic.php?f=39&t=6464&sid=7966a823f22e445ad1a3c… All best wishes, John -- Professor John R Helliwell DSc

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phenix install/splash screen issue
by Hekstra, Doeke Romke 15 Jun '25

15 Jun '25

Hi, After an ostensibly error-free installation of phenix-2.0-5716 on linux within an HPC environment, when starting the Phenix GUI, I get the following error: [dhekstra@holygpu7c26105 phenix]$ phenix Error in sys.excepthook: Traceback (most recent call last): File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 972, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 136, in OnInit self.start_gui() File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 151, in start_gui self.get_screen_params() File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 263, in get_screen_params self.set_window_height(self.prefs.get_root().gui.max_dialog_height) File "/n/hekstra_lab/garden_2/phenix/lib/python3.9/site-packages/wxGUI2/App.py", line 266, in set_window_height if (max_height < self.screen_height) : TypeError: '<' not supported between instances of 'NoneType' and 'int' OnInit returned false, exiting... ==== The same error occurred with phenix-2.0-5716 (both using the Linux-x86_64 installer). Could you please advise? Thanks, Doeke

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phenix.map_sharpening - sequence file required?
by Oliver Clarke 04 Jun '25

04 Jun '25

Hi, The new-ish map_sharpening utility seems to absolutely require a sequence file (at least on the CLI), whereas using auto_sharpen one could directly provide solvent content or estimated molecular mass. This option - molecular_mass - is still present in map_sharpening, but the program still terminates with an error - "Sorry: Need a sequence file". Is this intended? I run using the following command: phenix.map_sharpening cryosparc_P4_J199_002_volume_map.mrc resolution=2.3 molecular_mass=50000 Cheers Oli

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Reminder: Macromolecular Crystallography - CSHL Course October 2025
by Paul Adams 03 Jun '25

03 Jun '25

Dear Colleagues, A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 12-28th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. Many applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> Macromolecular Crystallography <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> October 12 - 28, 2025 Applications Due: July 15 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia Topics Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) For further information and to apply please visit the Macromolecular Crystallography course website. <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001xAZ7m1eA3JZFfHqguTfKfkZyzYIhmaBgv9…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road | Cold Spring Harbor, NY 11724 US Unsubscribe <https://visitor.constantcontact.com/do?p=un&m=001S3f9XM7Br7nKhcnZ-APDwA%3D&…> | Update Profile <https://visitor.constantcontact.com/do?p=oo&m=001S3f9XM7Br7nKhcnZ-APDwA%3D&…> | Constant Contact Data Notice <https://www.constantcontact.com/legal/customer-contact-data-notice> -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Windows 10 Retirement Date
by Billy Poon 27 May '25

27 May '25

Hi everyone, Microsoft will be dropping support for Windows 10 later this year on October 14, 2025. https://learn.microsoft.com/en-us/lifecycle/products/windows-10-home-and-pro Phenix intends to drop Windows 10 support after that date. Are there users where Windows 10 support is required after that date? Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: map-to-model FSC on low resolution map
by Pavel Afonine 26 May '25

26 May '25

Hi Jesse, there was a bug a while ago that we fixed. Are you using the latest Phenix? If not, please try it and if that does not fix the problem we'll take a closer look. All the best! Pavel On 5/26/25 08:07, bluufive2--- via phenixbb wrote: > _______________________________________________ > 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

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