March 2025 - ChimeraX-users - RBVI Mailing Lists

Focus in ChimeraX
by Luca Pellegrini 10 Oct '25

10 Oct '25

Hi, What is the ChimeraX equivalent to the Focus command in Chimera? I have selected a portion of a structure, and would like to bring it into focus without dragging it into view. Also Focus would automatically set the selection as the pivot point. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA lp212(a)cam.ac.uk

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Determining Chirality
by steffen＠sthomas.de 20 Jun '25

20 Jun '25

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Model loops with MODELER in ChimeraX
by Alexandra Zahradnikova 17 Jun '25

17 Jun '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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[ISOLDE] Handling Lys-Asp iso-peptide bonds and D-amino acids
by Yang Lee 22 Apr '25

22 Apr '25

Addressing this to Tristan, in all likelihood. Is there a way of parameterising KD isopeptide bonds and D-amino acids? Perhaps a secret three letter code I can rename the residues to make them play nice? Unfortunately, I'm trying to model a peptide that has both of these exotic elements. Cheers, Yang

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Concatenating trajectories in ChimeraX
by Alexandra Zahradnikova 20 Apr '25

20 Apr '25

Dear All, I am new in molecular simulation and not very much experienced with ChimeraX. I did not find an easy way to concatenate trajectories (in my case, .xtc files from gromacs). Any suggestions would be welcome. 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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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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Create new attributes
by javisanchezdelrio＠gmail.com 31 Mar '25

31 Mar '25

Hello! I am trying to create a new attribute in a cif file called align_rmsd. For the example, assume I want all atoms to have this attribute equal to 5. For this, I am opening the file in ChimeraX and applying the following command: setattr atoms align_rmsd 5.0 create true type float With the following result: Assigning align_rmsd attribute to 145 items However, when I do "save new.cif" I don't see any new attribute in the loop _atom_site.align_rmsd nor any value equal to 5. How can I store this values in a new cif file so that I see the values equal to 5? Thank you in advance! Javier

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Downloading ISOLDE
by Ashley Gutierrez 28 Mar '25

28 Mar '25

Hi there, I am having a bit trouble downloading the ISOLDE bundle. While I can download the .whl to my computer, it will not open in ChimeraX. Please let me know if I am missing some commands in between, I am new to this system. Thank you (:

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Ligand flying movie in chimeraX
by Matzov Donna 26 Mar '25

26 Mar '25

Hello, I'm trying to create a movie in Chimerax similar to the "Ligand flying into unbound conformation" that was in the old Chimera movie tutorials (https://www.cgl.ucsf.edu/chimera/data/tutorials/movies08/moviemaking.html) I tried using the "reset" command, but it seems like it doesn't exist in ChimeraX. Is there a command that replaces it? Alternatively, I would be happy for any suggestion for how to get an effect similar to the flying ligand in ChimeraX. Thanks, Donna Donna Matzov, PhD Department of Structural Biology Weizmann Institute of Science The Shalev-Benami Lab<https://www.weizmann.ac.il/Structural_Biology/Shalev-Benami/home>

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Change location of .cache/ChimeraX ?
by James Vincent 24 Mar '25

24 Mar '25

Hello ChimeraX Devs/Users, Is there a way to specify the location of the .cache/ChimeraX directory? As far as I can tell it is always $HOME/.cache/ChimeraX (on Linux machines). I see no options or configs to change this. We are installing ChimeraX on a multiuser system and would like to add a plugin/ bundle to be available for all users ( ChimeraX_ScipionExtensions 1.3). Perhaps I missed this in the documentation, but is there a standard way to add plugins so that they are available for all users? Thanks, Jim

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