October 2025 - phenixbb - phenix-online.org

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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Problem when trying to install last nighlty build on Ubuntu 22.04
by emmanuel.bettler＠univ-lyon1.fr 06 Oct '25

06 Oct '25

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

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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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