- 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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