October 2026 - ChimeraX-users - RBVI Mailing Lists

ChimeraX Command for Rotating a PDB Chain While Keeping One End Fixed
by Sen, Anindito 07 Oct '26

07 Oct '26

Hi, What ChimeraX command can I use to rotate a PDB chain from position A to position B while keeping one end of the chain fixed at its original position? Regards Anindito Sen. Ph.D Microscopy and Imaging Center Texas A&M University 301 Old Main Dr College Station, TX 77843-2257 Office: ILSB Room 1133 Tel. 979-458-9881 fax: 979-847-8933 http://microscopy.tamu.edu<http://microscopy.tamu.edu/>

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morph command ignores ions in metalloproteins?
by Guillaume Gaullier 02 Oct '26

02 Oct '26

Hello, I am trying to make a morph between PDB entries 9SKS and 9SKT. The protein does what I want, but I can't find out how to include the active site :ZN in the interpolation. This ion is consistently numbered between both structures, and I give model numbers to the morph command, which should select the entire models including their ions. Nothing about this in the documentation. What am I missing? If interpolating ions with morph is impossible to do for some reason, then it would be helpful to list it in the "limitations" section<https://www.cgl.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations> of the command's documentation. Thank you in advance, Guillaume --- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Regementsvägen 10 752 37 Uppsala Sweden 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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displaying Cryo-EM volumes from CryoSparc
by Schliebe, Paula 01 Oct '26

01 Oct '26

Dear CryoSPARC Team, I am processing Cryo-EM data of a ribosome using CryoSPARC. When I check my volume in the CryoSPARC volume viewer, everything looks fine. However, after downloading the volume, I cannot display it properly in ChimeraX (see attached photo). I am currently using ChimeraX 1.12 and CryoSPARC 4.7.1. Previously, I worked with ChimeraX 1.9 and CryoSPARC 4.6.2 and did not encounter any problems displaying the volumes. I also tested this with an older processed map that I had downloaded a while ago. I can display this volume properly in ChimeraX. However, after uploading it to CryoSPARC (where it is also displayed correctly) and downloading it again, I encounter the same problems when displaying it in ChimeraX. I am not sure whether this is an issue with CryoSPARC or ChimeraX. I have tried different combinations of the software versions, but so far nothing seems to resolve the problem. I hope you can help me out. I have also contacted the CryoSPARC team regarding this issue. Kind regards, Paula [cid:image001.png@01DD5196.CE77E0D0]

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