- ChimeraX-users - RBVI Mailing Lists

ISOLDE installation error
by Zhou, Tongqing (NIH/VRC) [E] 27 Aug '25

27 Aug '25

Dear All, I am having problem install ISOLDE on a new MacBook. My ChimeraX version is 1.10rc202505310246 (2025-05-31). When installing from Toolshed, it says: ERROR: Could not find a version that satisfies the requirement ChimeraX-Core~=1.10.0 (from chimerax-isolde) (from versions: none) ERROR: No matching distribution found for ChimeraX-Core~=1.10.0 Best regards, Tongqing Tongqing Zhou, Ph.D. Principal Investigator and Chief Structural Virology and Vaccinology Section Structural Biology and Structural Bioinformatics Cores Vaccine Research Center (VRC), NIAID National Institutes of Health Building T40, Room 117 (Office) Building 40, Room 4609B (Lab, shipping) 40 Convent Drive, Bethesda, MD 20892 Office: (301) 761-7068 Cell: (240) 695-0536 https://www.niaid.nih.gov/research/tongqing-zhou-phd tzhou(a)nih.gov<mailto:tzhou@nih.gov>

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Displaying maps with threshold defined by mapstats
by Grundmann,Lorenz Emanuel 27 Aug '25

27 Aug '25

Dear ChimeraX-Team and all, I want to visualize multiple cryoEM maps in a comparative manner. Therefore, I would like to display them with a threshold level of e.g. 90% their maximum voxel value. Is this possible in chimerax? Any help would be greatly appreciated. Thank you. Best, Lorenz

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aborting slow hbonds command
by Daniel Larsson 25 Aug '25

25 Aug '25

Is it possible to prematurely stop a command issued on the command line that takes too long time? I often have sessions with many (more than 20) large ribosome structures open at the same time. I sometimes mistype the restrict atom-spec2 argument for the hbonds command and ChimeraX goes through each of the structures one by one twice, which can take very long time. I wish there were a flag to the hbonds command to only consider the models in atom-spec1, so that those typos does not spawn a search across all models. In addition, it would be great if the code for the hbonds command could be optimized. Why iterate over all models if only atoms in one model are in atom-spec1? Regards, Daniel 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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ISOLDE released for ChimeraX 1.10
by Tristan Croll 22 Aug '25

22 Aug '25

Hi all, Just a note for ISOLDE users: ISOLDE 1.10 is now out on the TooShed, ready for use with ChimeraX 1.10.x. Please enjoy! Best, Tristan -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

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Model-Map coloring using the ChimeraX
by Andrew Mugo 21 Aug '25

21 Aug '25

Dear ChimeraX user support team, I am having a problem of coloring map based on the model color. I uninstalled and re-installed ChimeraX 1.9/1.10 but when I try to color the map, the software gives electrostatic color like. Please let me know how I can solve this problem. Best regards, Andrew

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Residue Interaction Network visualisation using chimerax
by Gagandeep Singh 20 Aug '25

20 Aug '25

Dear team , I have generated residue interaction network (RIN) data using RING 4.0 and would like to visualize this . I am familiar with UCSF Chimera, which supports visualization of RIN data, and I was wondering if ChimeraX also offers similar functionality. Kind regards -- *गगनदीप सिंह **/ Gagandeep Singh* *डॉक्टरेट का विद्यार्थी **/ Doctoral student* *ब्रिक - ट्रासलेशनल स्वास्थ्य विज्ञान और प्रौद्योगिकी संस्थान* *BRIC- Translational Health Science and Technology Institute* *(भारत सरकार के जैव-प्रौद्योगिकी विभाग का एक स्वायत्त संस्थान)* *(An autonomous institute of the Dept of Biotechnology, Govt Of India)* *NCR Biotech Science Cluster,* *3rd Milestone, Faridabad–Gurugram Expressway,* *PO box #04, Faridabad- 121001 (Haryana)*

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Question about the software features
by Mazrouee, Sepideh (NIH/OD) [E] 19 Aug '25

19 Aug '25

Hi, I had the chance to use ChimeraX recently for aligning some predicted protein 3D structures and it looks wonderful. However, I need to do some labeling of the visualization (including labeling of specific protein domains) and I wasn't sure if such feature exists in the software or there might be a way to make it happen. I would highly appreciate your help if you could provide me with some online resources to educate myself or join a call with some team members to help us out. Best regards, Sepid Sepideh Mazrouee, PhD Researcher, Office of Data Science Strategy (ODSS) Office of Director, National Institute of Health (NIH<https://www.nih.gov/>)

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Select atoms/chains by _atom_site.label_asym_id instead of _atom_site.auth_asym_id?
by Ute Roehrig 19 Aug '25

19 Aug '25

Hello, Is there a way to select atoms/chains from a mmcif file by their _atom_site.label_asym_id value instead of the _atom_site.auth_asym_id value? Thank you for your help, Ute

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Question Regarding Contacts Command in ChimeraX
by Andrew Guo 19 Aug '25

19 Aug '25

Hello, My name is Andrew Guo, an undergraduate at the University of Maryland College Park, doing research under Dr. John Orban with help from Dr. Andy LiWang from the University of California Merced, in the field of protein fold switching. Dr. LiWang recently used ChimeraX to calculate vdW contacts closer than 3.8 A between carbons in the context of a fold switching region in a small list of 26 "metamorphic" proteins (see here <https://doi.org/10.1073/pnas.2422725122>). I am now working on automating the whole process of calculating these contacts. In doing so, I have encountered a strange inconsistency that I do not know how to fix, and was hoping to gain some insight from the people who have developed ChimeraX. Previously, the overall contacts count was calculated by first calculating interdomain contacts then intradomain contacts and summing the two. It would be much simpler to calculate the contacts in one "whole" command instead of restricting the command to just interdomain or intradomain contacts. However, I have found that this "whole" command sometimes includes ligand contacts. For instance, for the pdb code 4O01A and region of interest residues 446-478, I have the following set of commands: interdomain: contacts /A:446-478@C* restrict /A:1-445,479-506@C* distance 3.8 reveal true name vdW output 13 intradomain: contacts /A:446-478@C* restrict /A:446-478@C* distance 3.8 reveal true name vdW output 8 "whole": contacts /A:446-478@C* restrict /A@C* distance 3.8 reveal true name vdW output 22 Obviously, 13 and 8 do not sum to 22. Ligand command: contacts /A:446-478@C* restrict ligand distance 3.8 reveal true name vdW This ligand command had an output of 1 and was the following: /A LEU 463 CD1 /A LBV 600 CMA (alt loc A) This contact was also the extra contact found in my "whole" command output, so I could just run the two commands (whole and ligand) and subtract the output of the ligand command from the output of the whole command. However, for the pdb code 3KMZA and region of interest residues 393-421, I have the following: interdomain: contacts /A:393-421@C* restrict /A:1-392@C* distance 3.8 reveal true name vdW output 0 intradomain: contacts /A:393-421@C* restrict /A:393-421@C* distance 3.8 reveal true name vdW output: 1 distances atom1 atom2 distance /A MET 400 CG /A GLU 401 C 3.788 "whole": contacts /A:393-421@C* restrict /A@C* distance 3.8 reveal true name vdW output: 1 distances atom1 atom2 distance /A MET 400 CG /A GLU 401 C 3.788 ligand: contacts /A:393-421@C* restrict ligand distance 3.8 reveal true name vdW output 6 1-6 = -5 contacts Using my method, I get -5. Clearly, this is bad. The ligand command gave these 6 contacts: 6 distances atom1 atom2 distance /A THR 397 CG2 /A GOL 3 O3 3.321 /A ARG 394 CD /A GOL 3 O2 3.411 /A ILE 396 CA /A GOL 3 O3 3.436 /A ILE 396 CG2 /A GOL 3 O2 3.667 /A ILE 396 C /A GOL 3 O3 3.703 /A ILE 396 CB /A GOL 3 O3 3.721 However, these contacts were not part of the output of the whole command, unlike in the case of 4O01A. Is there something I am doing wrong with how I am setting up my commands? Please let me know if further information is needed! Thank you, Andrew

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Log Setting
by NUR AIDA SAKINAH 18 Aug '25

18 Aug '25

Hi ChimeraX teams, I am using ChimeraX version 1.9 in dark theme, when open the saved session, the log shown in highlighted grey colour if i’m not mistaken. So, is there a setting to make it easier to view the log for the saved session? Thank you. Regards, Aida

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