- phenixbb - phenix-online.org

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

5 4

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 ------------------------------------------------------

1 0

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

2 2

Generating BIOMT record for icosahedral symmetry
by Lei Chen 05 Oct '25

05 Oct '25

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

4 7

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

1 0

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

1 0

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

3 3

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,

2 1

[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

4 4

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>

1 0