February 2025 - ChimeraX-users - RBVI Mailing Lists

What is the .exe file for ChimeraX Toolbox?
by m.i.bashir＠bham.ac.uk 11 Mar '25

11 Mar '25

Hi all, First time posting here. I'm looking to find the name and location of the file/folder that manages the ChimeraX in-app browser. The way I launch the browser is to go to 'tools' in the top bar, then press 'more tools', and then it brings up the ChimeraX Toolshed Where is the .exe file that controls this in app browser? I am attempting to find the .exe file and black list it, so we can use ChimeraX for an exam Thanks,

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define integer attributes for multiple individual pseudobonds
by hannes.ludewig＠googlemail.com 28 Feb '25

28 Feb '25

Dear developers, I am trying to color pseudobonds by an individual (per-bond) attribute value (integer). I seem to be unable to use .pb files to create individual pseudobonds. And when I am using the pbond command several times providing an individual name for each pseudobond thus creating individual models (#1.1, #1.2, etc) I am unable to assign an attribute and color all pseudobonds according to the corresponding attribute value. What I want to create is similar to the alphafold contacts colored by PAE. Only that the values I am providing aren't PAE and I would like to determine the residue pairs that form each pseudobond. I apologize in case I am overlooking something obvious, but your help and/or clarification would be very much appreciated. Thank you. Best wishes, Hannes

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Disulphide bridges in ISOLDE
by Guillaume Gaullier 28 Feb '25

28 Feb '25

Hello ISOLDE users and Tristan, Is there a distance threshold at which ISOLDE won't let me close a disulphide bridge? I am puzzled, because it seems I can close a disulphide between two Cys about 10 residues apart in sequence and quite far from each other in space. In fact much further apart than a bond length, so the resulting bond looks ridiculously stretched. But it is quickly fixed when running a local simulation, even if it needs to pull the backbone out of density to achieve a reasonable S-S bond length. In the same model, I have two other Cys that follow each other in sequence. When loading the AlphaFold prediction, the two S atoms are close enough (for some reason) that ISOLDE offers to make the disulphide, so I say yes. Later on, wanting to test both options to assess which one is best supported by the map, I can break this disulphide, but once I do there is no way to close it again. In this case, the two S atoms settle about 3.4 Å apart when removing the bond, which is longer than an ideal disulphide, but much shorter than the distance over which ISOLDE still allowed me to form a disulphide in the first case. The documentation doesn't say anything about disulphides (or somehow I missed it). In fact, there seems to be no command to operate on disulphides? Using the menu item does not write anything to the Log, so if there is a command I cannot find what it is and what options it might accept. If someone can help with this, I would appreciate it! Thank you, Guillaume --- Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Lägerhyddsvägen 1 752 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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Assistance Required: Extracting List of Interacting Residues within 4 Å in UCSF Chimera
by Rashmi Aggarwal 27 Feb '25

27 Feb '25

Dear UCSF Chimera Support Team, I hope this message finds you well. I am currently working on analyzing interactions between two molecular structures using UCSF Chimera. I have successfully identified residues that are within a 4 Å distance between the two molecules. However, I am encountering difficulties in obtaining a clear, textual list of these interacting residues, as reading them directly from the visual representation is challenging. Could you please provide guidance on the specific commands or procedures within Chimera that would allow me to: 1. *Select residues* in one molecule that are within 4 Å of the other molecule. 2. *Generate and export a list* of these selected residues for further analysis. I have attempted various selection and reporting commands but have not yet achieved the desired outcome. Detailed instructions or references to relevant documentation would be greatly appreciated. Thank you very much for your assistance. Best regards, Rashmi

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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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Cannot click popup windows in ChimeraX WSL installation
by Jobichen 27 Feb '25

27 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 25 Feb '25

25 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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