April 2025 - ChimeraX-users - RBVI Mailing Lists

Can't open ChimeraX on my Win11
by kangkang042＠126.com 07 Apr '25

07 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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Model loops with MODELER in ChimeraX
by Alexandra Zahradnikova 02 Apr '25

02 Apr '25

Hello, I have recently watched a Youtube video (https://www.youtube.com/watch?v=GV6jHhxR5T4) about completing loops with Modeller in ChimeraX. However, the structure I want to model is only a part of the actual molecule, and I want to replace one unresolved segment (300 residues long) with 11 glycines. When I upload both, the FASTA file with the sequence as it should look after completion of the loops, and the PDB file of the incomplete structure, I am not able to align them together in order to perform the modelling. - If I use the original PDB file containing the SEQRES part, the association is performed but produces mismatches after the start of the unresolved sequence. - If I use the PDB file without the SEQRES part, I am not able to perform the association. Can anybody help me? 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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