- ChimeraX-users - RBVI Mailing Lists

Cannot click popup windows in ChimeraX WSL installation
by Jobichen 26 Feb '25

26 Feb '25

Hi All,I am unable to click on any popup windows in my chimeraX installation. For eg: colour menu, once popped up, unable to click on any options.Ubuntu 22.04.5 LTS installed under WSL in Dell laptop. ChimeraX ver 1.9Error messages:NOTE: available bundle cache has not been initialized yetmalloc(): unsorted double linked list corruptedAborted (core dumped) Any suggestions.Thank you.Jobi

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Rotation using left mouse button
by y.v.hazendonk＠nki.nl 26 Feb '25

26 Feb '25

Hello, In my work with ChimeraX I have to rotate my proteins quite a lot to get a good look at different residues and helices. My problem is that very often when I am rotating my protein using the left mouse button, another piece of my protein will glide across my screen in the foreground, at which point the axis of rotation will lock onto this other piece. Is there a way to disable this unwanted locking? I am fine with these pieces floating across the foreground, as long as my axis of rotation doesn't suddenly lock onto them. I want the rotational axis to stay where it was when I started rotating. I look forward to your reply on how to fix this issue. Thank you in advance. With kind regards, Yorick van Hazendonk

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Communicate between multiple ChimeraX instances
by Roden Deng Luo 25 Feb '25

25 Feb '25

Hi, I wonder if there is a way to synchronize two or more ChimeraX instances/sessions. For example, sync the camera. The meeting command ( https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/meeting.html) a great command I just got to know, is very close to what I am looking for. Only I will have different data in different instances, and toggles to enable and disable what features to be synced. If it is not currently implemented, how should I approach it as a developer? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Measure angle between domains in chimeraX
by junjie han 24 Feb '25

24 Feb '25

Hi Elaine, I hope this email finds you well. May I ask how to measure the angle between two domains from one molecule or two different molecules in ChimeraX. Here are some examples below. Example 1: [cid:ee5ac0af-a9be-4e98-bb7c-e555c8f183c2] How to calculate these angles (54°, 38°)？ Example 2: [cid:24512415-5303-4be2-8f61-a4fd6acdc0ee] How to calculate this angle (75°) ? Example 3: [cid:f3ed355d-a961-4647-8a3c-b39ab3875cb8] How can I measure the rotation angle between A and B, or between two specific regions of these two molecules in ChimeraX? If I need to calculate the rotation angles of two molecules relative to a specific molecule, how can I define a shared axis for calculating the rotation angles? The rotation axes are different when I use the command “measure rotation A toModel B” to calculate the rotation angles, which is not an ideal way to compare them in parallel. Thank you in advance for your any suggestions. Very appreciated, Junjie

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Trouble Morphing 2 Proteins
by Andrew Mejia Garnica 24 Feb '25

24 Feb '25

Hello, I have been using ChimeraX with a mac book from 2020 with a 1.1 GHz Dual-Core Intel Core i3, Intel Iris Plus Graphics 1536 MB and 8 GB of RAM. Everything seems to be working fine until I try to do a morph. Both proteins have been super positioned by matchmaker. I can only complete 5 frames out of the 60 with the command, morph #1,2 wrap true frames 60. However, I am not able to look through the frames, record or press play. I have tried it with the tutorial proteins as well and got stuck. The proteins that I am trying to morph will be attached to this email. I would like to ask if you could do a morphing for me or redirect me to be able to. I would also like to ask if it is a Graphis problem as I was also unsuccess full using a Dell laptop with a , 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHZ, 16GB of RAM, 64-bit operating system, x64-based processor. Thank you for your time and I hope to hear from you soon. Best, Andrew

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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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Freelance vs. Agency – Best Choice for Native App Developers Houston?
by hooria.khan＠algoace.com 23 Feb '25

23 Feb '25

I’m trying to decide whether I should hire a freelance developer or work with an agency for my native app development needs. Freelancers can be more affordable, but agencies offer structured project management. Are there any experienced <a href="https://algoace.com/houston-app-development/">Native App Developers Houston</a> who work independently and provide top-notch services? On the other hand, if you’ve worked with an agency, was the cost worth it? Any recommendations based on your experience?

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Update chain description from fasta file
by Paul Sauer 23 Feb '25

23 Feb '25

Hi, I really like the 'sequence update' feature that was introduced in Chimerax 1.9. I was wondering if it is possible to expand the capability of this command to update the sequence description/ sequence name from the header line of an opened alignment or fasta file and write it out with the cif file. It seems like currently the full sequence is updated from an associated fasta file but the sequence names are being ignored. Could the sequence name written into the ' entity.pdbx_description' column in the resulting cif file? Or maybe there is already an option that I missed? Also, as a secondary feature request, maybe the sequence update command could not only write the ' entity_poly.pabx_seq_one_letter_code_can' table but also use the available coordinates and residue names of the structure to write the '_entity_ poly.pdbx_seq,_one_letter_ code' table for each polymer that includes modified residues/ligands etc in parentheses in addition to the canonical one letter code where known. I could imagine that these capabilities would make depositing coordinates of macromolecular complexes with many chains to the PDB much easier and more interactive, so maybe this would be helpful for other people as well. Thank you to the Chimerax team & contributors for creating such a great program, Paul

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Dear ChimeraX users!
by amiraziznezhad＠gmail.com 23 Feb '25

23 Feb '25

Dear ChimeraX users! I am dealing with the analysis of protein-ligand interactions in a single PDB structure. I am looking for any tools implemented in Chimera-X, which could be used to analyse the interactions (besides the hbond and contact tools giving info in the log files msuic). I wonder to know which commands and corresponded ChimeraX tools could be used to produce the 2D contact diagrams shown on the Fig.4 as well as python graphs demonstrated on the Fig.5 in the Chimera-X article: https://www.myeasymusic.ir/ Many thanks in advance! Cheers Enrico

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RspProp
by Robert Stanley 23 Feb '25

23 Feb '25

Hello - I was wondering what I have to do to install the RspProp tool? It doesn't appear in my utilities menu or the structure analysis one. I have version 1.9 (2024-12-11). I very much appreciate this program and use it in my Biochem and Biophysical Chemistry courses to expose the students to it ASAP. Thanks, Bob Stanley Robert J. Stanley, Ph.D. Professor of Chemistry 1901 N. 13th St., 250B Beury Hall Temple University Philadelphia, PA 19122 (215) 204-2027 https://www.cst.temple.edu/~rstanley/

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