April 2025 - ChimeraX-users - RBVI Mailing Lists

Refinement in ISOLDE failing
by Firdous Tarique 09 Apr '25

09 Apr '25

Dear everyone I am trying to refine my protein using ISOLDE in ChimeraX which is failing with the following error. "At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been parameterised. Launching the unparameterised residue widget to help sort this out." The protein contains two heme molecules and Ca ions which obviously is the reason why it is failing. Once these molecules are deleted it runs fine. My question is how to add that specific MD force field for these molecules in order to run the ISOLDE in ChimeraX. Any input would be appreciated. Firdous

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Re: issues with writing models as pdb files
by arangarajan＠initialtx.com 08 Apr '25

08 Apr '25

Hi everyone, I noticed that sometimes when i write pdb of one model or a selection , it does not open in other programs.( MOE,Pymol). One of the errors i noticed recently was that th pdb file was written as a multi model pdb file ( each of the 70 residues in the protein were separate models) , i cleaned it using notepad++ by removing the model lines and it was opening correctly. i was told that it might be related to using split command. i use split often and it might be the case. can some one please explain how using split can lead to this? and if so what is best way to fix it? should i perhaps run some version of combine command on the model prior to writing it out as pdb file. thanks again, best amith

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Can't open ChimeraX on my Win11
by kangkang042＠126.com 08 Apr '25

08 Apr '25

About 2 weeks ago, it worked fine. Today when I click the ChimeraX startup, nothing happened. I reinstalled the lastest version v1.9, nothing changed. Run ChimeraX-console.exe in cmd, it shows these information: NOTE: Traceback (most recent call last): File "<frozen runpy>", line 198, in _run_module_as_main File "<frozen runpy>", line 88, in _run_code File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\\__main__.py", line 1217, in <module> exit_code = init(sys.argv) ^^^^^^^^^^^^^^ File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\\__main__.py", line 653, in init sess = session.Session( ^^^^^^^^^^^^^^^^ File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\core\session.py", line 551, in __init__ from chimerax.graphics.gsession import register_graphics_session_save File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\graphics\\__init__.py", line 37, in <module> import chimerax.arrays File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\__init__.py", line 24, in <module> from ._pyarrays import get_lib, get_include, load_libarrays File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\_pyarrays.py", line 40, in <module> from . import _arrays ImportError: DLL load failed while importing _arrays: 找不到指定的模块。 BUG: ImportError: DLL load failed while importing _arrays: 找不到指定的模块。 File "E:\chimeraX\installation\bin\Lib\site- packages\chimerax\arrays\\_pyarrays.py", line 40, in from . import _arrays _See log for complete Python traceback._ My PC: Win11 Pro Workstation 26100.3624

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How to browse inspect ligands?
by Guillaume Gaullier 04 Apr '25

04 Apr '25

Hello ChimeraX team, These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands. Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand. I looked for something like this, but couldn't find anything. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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saving cloned structures on chimerax inquiry
by Joel Gallardo 03 Apr '25

03 Apr '25

to whom it may concern, i have mapped out a mol2file onto a structure found in a .mrc file. and then i ran this command to multiply the mol2 structure: sym #2 h,0.357979,132.83196,72,-40 coord #1 center 119.04,119.04,119.04 it multiplied it as intended which is good but now i want to save those multiplied mol2 files into a sperate mol2 files. i tried this command: save multiplied_structures.mol2 format mol2 models #2 but this only saves a single mol2 structure into the new mol2 file. i want all 72 molecules in one mol2 file. can you give me some advice as to how i may be able to do this? my ultimate goal is to take that mol2 file and do an md simulation. Best, Joel Gallardo (Graduate student in chemistry)

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Keeping track of H-bonds in trajectories
by Alexandra Zahradnikova 02 Apr '25

02 Apr '25

Hello, I am new in molecular simulation and not very much experienced with ChimeraX. Is there a way to keep track of H-bonds between two specific residues (they can form one or more H-bonds) during the course of the trajectories (in my case, .xtc files from gromacs)? Thanks in advance Sasha ________________________________________________________________________ Alexandra Zahradníková, PhD Department of Cell Cardiology Institute of Experimental Endocrinology Biomedical Research Centre SAS Dúbravská cesta 9 845 05 Bratislava Slovakia Mobile: +421 908 069 796

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