March 2025 - phenixbb - phenix-online.org

Differential density peaks and hydrophobic residues
by Lucas Souza 04 Apr '25

04 Apr '25

Hi everyone, I am refining a ~3A structure using phenix 1.21.2-5419. I am at the final stages of the refinement but I am seeing some positive density on some hydrophobic residues (mainly Ile and Leu) together with a negative density around those residues (image attached). At first, I guessed that might be related to solvent mask, so I turned on optimize_mask. That did not solve the issue, although slightly decreased R values. Diffraction data was processed with autoproc+staraniso and does not seem to be twinned (normal intensity stats + map deteriorates if twinning refinement is applied). Does anyone have a guess about that? Best, Lucas -- Lucas Souza dos Santos Laboratório de Biologia Estrutural Aplicada (LBEA) Departamento de Microbiologia Instituto de Ciências Biomédicas II - USP Cidade Universitária - São Paulo - SP CEP 05508-000

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CloudFlare and Spain
by Billy Poon 31 Mar '25

31 Mar '25

Hi everyone, Does anyone in Spain have issues reaching the Phenix website ( https://phenix-online.org)? Our website is behind CloudFlare and it looks like, periodically, some CloudFlare IP addresses are blocked in Spain due to some piracy 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

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IBA2025 - May 5&6 2025 - Cambridge MA
by Chip Lesburg 30 Mar '25

30 Mar '25

The Industrial Biostructures America conference will take place on May 5 & 6, 2025 at the MassBioHub in Cambridge MA. The conference was launched in 2018 to bring the industry-based structural biology community together for two days of presentations and networking. This is a great place for industrial structural biologists, as well as those who are industry-curious. The conference will feature keynote presentations by: * Dr. Stephen K. Burley, Director RCSB Protein Data Bank and Rutgers University Professor * Dr. James Fraser, Professor and Chair Department of Bioengineering and Therapeutics Sciences at UCSF * Dr. Stephen Harrison, Professor Harvard Medical School/Investigator Howard Hughes Medical Institute * Dr. Mark Murcko, Founding CSO/Board Member at Dewpoint Therapeutics and Relay Therapeutics Conference information is available at https://industrialbiostructuresamerica.org along with guidelines for submitting abstracts for scientific presentations during the conference. Scientific sessions will cover the following topics: * Structural Biology of Targeted Protein Degradation: Glues, TCs & DUBs * Developing Fragments to Drugs: Challenges & Victories * Molecular Dynamics and Allostery - Bridging Experimental and Computational Drug Discovery * Membrane Protein Structure Guided Design * CryoEM Synergies with Molecular Modeling and Computational Models * Biologics (Antibody Design & ADCs) * AI/ML in Structural Biology and Drug Discovery * Hot Topics (SBDD, Kinases, RNA) The abstract deadline is April 1. Space is limited so if you're interested, please register soon. Contact us at iba(a)proteros.com<mailto:[email protected]> for information regarding Exhibitor and Sponsor opportunities [cid:logo_c70edd4a-e7f0-4d54-be6f-d03f53f0c961.png] Charles Lesburg Vice President, Structural Biology odysseytx.com<https://protect.checkpoint.com/v2/___https:/odysseytx.com/___.YzJ1Om9keXNzZ…> This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender.

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can not launch phenix gui
by lzhlizehou＠outlook.com 29 Mar '25

29 Mar '25

Dears, I am using Ubuntu 24.04 and have successfully installed phenix-1.21.2-5419. However, when I attempt to launch the GUI by running the phenix command, it fails with the following error: Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 961, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/phenix-1.21.2-5419/modules/phenix/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 "/usr/local/phenix-1.21.2-5419/build/../modules/phenix/wxGUI2/command_line/main.py", line 34, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.21.2-5419/build/../modules/phenix/wxGUI2/command_line/main.py", line 28, in run wxapp = App.PhenixApp(args) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 84, in __init__ wx.App.__init__(self, 0) File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 118, in OnInit show_splash_screen(timeout=2000) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 1015, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. Looking forward to your reply. Best regards Li

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Call for Abstracts - Combining experimental data with predicted models - Session at the ACA Meeting, July 18-23, 2025
by Christopher Williams 24 Mar '25

24 Mar '25

Dear All, Rakhi Rajan and I are co-chairing the session "Combining experimental data with predicted models for structure determination" session at the 75th American Crystallographic Association Meeting in Lombard, IL (near Chicago) from July 18–23, 2025. It's a great meeting, and we encourage both general attendance and submissions for our session. We welcome abstract submissions for both talks and posters. If you're interested, please submit your abstract at https://www.acameeting2025.com/. Deadlines are fast approaching: March 31 – Deadline for oral abstracts & travel grant applications April 30 – Deadline for poster abstracts We invite contributions of novel methods and pipelines for combining prediction and experiment. We also invite stories of working with predictions and data. Have you gotten into the weeds with AlphaFold? Has structure prediction let you better design an experiment? Or has experimental data revealed an important detail missing from prediction? We want to hear about it! If you're interested in sponsoring our session, please reach out as well. -Christopher Williams ---Richardson Lab, Duke University -Rakhi Rajan ---University of Oklahoma

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Issues with zero B-factor and ADP refinement
by sylee00＠snu.ac.kr 23 Mar '25

23 Mar '25

Dear all, I am encountering issues related to B-factors and ADP refinement in Phenix and would appreciate any insights or suggestions. I am currently working on my first PDB file, but I've noticed that many atoms in the PDB file have a B-factor of 0. As far as I understand, B-factor values are calculated by ADP refinement in Phenix real-space refinement, but even after running real-space refinement (with ADP on in refinement settings), the B-factor remains 0 for many atoms. I am currently using Phenix 1.20 on Windows (Newest version available on window). I also attempted to run Phenix 1.21 on a Linux in other computer, but when ADP refinement is enabled, the process starts normally but halts during the ADP refinement step. So I couldn't test whether the issue is fixed in the newest version. Aside from the B-factor issue, I am also experiencing an inssue related to ADP refinement: When I run real-space refinement with ADP refinement enabled, the process starts normally but halts during the ADP refinement step. According to the log file, other refinement steps proceed without issues, but it fails to progress at the ADP refinement stage. Additionally, when I try to pause the process, I receive a "NoSuchProcess" error, so ADP refinement process may have unexpectedly terminated. At first, I thought it's the issue related to system performance or hardware differences, because adp refinement with this pdb file and identical parameters works on some computer but fails on others (the same version of Phenix). Still it's weird because this issue has occurred unexpectedly, as ADP refinement previously worked in my computer under the same conditions without any problems and also other PDB files run without any problems in my computer. I would appreciate any insights or suggestions on how to resolve this. Thanks

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phenix low resolution refinement strategies
by a131943017＠163.com 20 Mar '25

20 Mar '25

Hi, how do I set the optimization parameters to make free R lower for 3.2Å x-ray crystallography data, or in other words, how do I go about determining whether the optimization strategy is appropriate or not? Questions from a Phenix Beginner.

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seeking help for phenix - coot model building
by tim smith 20 Mar '25

20 Mar '25

Hi everyone, I’m currently working on building a model and have encountered some difficulties with the map-model process. I would greatly appreciate it if anyone could assist me in either helping to build the model or teaching me how to do it. I’m happy to offer a suitable reward for your time and help. Thank you in advance for considering! Regards, Stim

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CSD changes conformation to planar during phenix.refine
by Andrea Smith 20 Mar '25

20 Mar '25

Hi all, I have a structure where I clearly see that one of the cysteines is oxidised. I have modelled CSD instead of CYS and when I do real space refine in Coot, the CSD sits nicely in the density. When I submit the phenix.refine job, I can see that the geometry changes and now the SOOH is planar. I tried to add the CSD.cif from PDB into phenix.refine as restraints, but it doesn't help and during the automatic refinement the geometry is changed to planar again. Anyone experienced same thing? What do I do? Thank you, Andrea

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Trouble with GTP/GDP refinement.
by DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO 18 Mar '25

18 Mar '25

Dear phenixbb: I'm working with a GTP binding protein and have had some problems running phenix_refine. In my unit cell there are two molecules one with GDP and one with GTP, which I added in Coot(0.9.8). When refining the following error message pops-up : "Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols:4 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modifications and apply_cif_link parameter definitions if necessary". Checking the log file I found that the problem seems to be hydrogen atoms from these ligands Number of atoms with unknown nonbonded energy type symbols: 4 "HETATM 6499 H5' GTP A 501 .*. H " "HETATM 6502 H5'' GTP A 501 .*. H " "HETATM12939 H5' GDP B 501 .*. H " "HETATM12940 H5'' GDP B 501 .*. H " Including the corresponding .CIF files (dowloaded from PDB) did not solve the problem and the same error popped. Since I'm in the initial stages of the refinement I'm running phenix with bindividuals. Could anybody save my day giving me some light into this issue? Cheers, Diego

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