January 2025 - ChimeraX-users - RBVI Mailing Lists

ISOLDE and secondary structure restraints
by Guido Hansen 25 Feb '26

25 Feb '26

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

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Volume eraser as cube?
by Oliver Clarke 25 Feb '26

25 Feb '26

Hi all, Hope the chimeraX team & community are having a great start to 2025! There are often situations (in single particle cryo-EM) where I would like to erase using a plane rather than a sphere - e.g., when I want to chop off density protruding from a nanodisc or micelle in order to make a mask. There are various workaround ways to do this (e.g. just making the sphere enormous, making a cubic/rectangular mask and multiplying/substracting, etc), but I was wondering if this is a common enough scenario (perhaps other users can chime in?) that it might be worth adding the option of erasing using a cube rather than a sphere? Cheers Oli

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ChimeraX version 1.9 has been released
by Elaine Meng 23 Jan '26

23 Jan '26

UCSF ChimeraX version 1.9 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.8 (June 2024) include: - Foldseek search and analysis of large sets of similar structures - Find Cavities tool and "kvfinder" command to identify pockets and channels in macromolecules - optional residue-level summaries of H-bond and contact calculations - "mutationscores" command for analysis and plotting of results from deep mutational scanning - "surface hidefarblobs" command for colocalization analysis of light microscopy channels - raycasting option for medical images or other maps displayed as transparent volumes - selection can be expanded to all residues associated with the same column(s) in a sequence alignment - protein structure metadata can be updated with full chain sequences - missing-structure pseudobonds are labeled with the number of missing residues (default, can be turned off in preferences) For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

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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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Show side chain, main chain, and cartoon at the same time
by Zhang, Miao 27 Feb '25

27 Feb '25

Dear colleagues I am new to ChimeraX. I am trying to figure out how to show side chain, main chain, and cartoon at the same time in a protein structure. Like the one below made in other software. Could you please help? [cid:image001.png@01D9D154.CE3D4440] Best, - - - - - - - - - - - - - - - - - Miao Zhang Ph.D. Associate Professor Chapman University School of Pharmacy 9401 Jeronimo Rd, Suite 297W Irvine, CA 92618 Phone: 714-516-5478 http://www.chapman.edu/our-faculty/miao-zhang

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Surface dust command in the .cxc script
by 李泽 24 Feb '25

24 Feb '25

Hi all: I'm trying to use the .cxc script to run the software, I found that the "surface dust" command has never been executed in it. Have anyone met the same problem? Any suggestions. Thank you all. Best, Ze

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assistance on bundle writting
by Nguyen, Catherine 14 Feb '25

14 Feb '25

Hello, I was hoping to get your help. I am trying to write a bundle and I am struggling to figure out how I can add psuedo-bonds using python as I want to connect two amino acids by the CA. Would you be able to help me find a way to do this? I hope to hear from you soon, Best wishes, Catherine

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Get color code of a custom color
by Ahmad Khalifa 11 Feb '25

11 Feb '25

I created a custom color that I want to use in a different session. is there a way to do that besides trying to match colors by eye? Regards.

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Double and Triple Bond Stick Style
by Smith, Chase 05 Feb '25

05 Feb '25

Dear ChimeraX, I was just wondering why there is no way to represent a double or triple bond in either the ligands or the protein amino acids when viewing as a Stick or Ball-and-Stick representation? I sometimes use Chimera or ChimeraX to make visuals for my lectures, and the students often have difficulty in understanding due to the absence of the multiple bonds. I would love to have the ability to represent the double or triple bonds with multiple lines between the atoms. Thank you, Chase Smith ... ChaseSmith, PhD Chair, Department of Pharmaceutical Sciences & Associate Professor of Medicinal Chemistry School of Pharmacy MCPHS University 19 Foster Street | WorcesterMA01608 T 508.373.5717F 508.890.5618C 978.855.7203 chase.smith(a)mcphs.edu www.mcphs.edu MCPHS University Confidentiality Note: This e-mail, and any attachment to it, is intended to be confidential and might be legally privileged. It is intended solely for the use of the addressee. If you are not the intended recipient, you are hereby notified that reading, copying, disseminating or distributing this email is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.

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