May 2021 - ChimeraX-users - RBVI Mailing Lists

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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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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Quest 2 Support?
by Blaine Hewitt 27 Dec '24

27 Dec '24

Hello, my name is Blaine Hewitt. Now I know that you have stated previously that you have no intention of bringing support to the Oculus Quest. Which is completely understandable since I know that not only would you have to develop around a completely new Operating System but another CPU architecture and much much more I assume. But with the soon release of the Oculus Quest 2 and it's new XR 2 chip-set makes a pretty good argument for it. As this would allow for much easier use in education (as is what I am attempting to do with it). I think it will be even easier now to push updates with SideQuest <https://sidequestvr.com/> being relatively simple to setup. I know that another (Naome <https://blog.matryx.ai/nanome-on-quest-public-beta-is-now-available-b546321…>) program is already available on the platform. But I do like your program a lot more since it is able to be used for free unlike Nanome Pricing <https://nanome.ai/pricing/> which is... as to say unappealing to public schools (such as mine). I was was also thinking (sorry if I am becoming annoying at this point) that if you do make a version of the Quest that you could make that GitHub branch available to the public. As for example while I may not be great at understanding complex protein structures I can help to make the whole experience more user friendly. Anyways if you read this far thank you for taking time from your day to read this. If you want to know who I am, my name is Blaine I am in my senior year of High School (Waynecsd <https://wh.waynecsd.org/>). I have to do a project by the end of the year where I have to present an area of study I want to pursue and I decided to research the effects of VR on the human's ability to learn and retain information. Budget..... None

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Apple silicon (M1 chip) native version?
by Jeffrey D. Hartgerink 28 Apr '22

28 Apr '22

Are there any plans for an Apple Silicon (M1 chip) native version of ChimeraX? While things work ok via the Rosetta emulator, it would be great to have the performance from a native app. -------------------------------------- Jeffrey D. Hartgerink, Ph.D. Prof. of Chemistry and Bioengineering Rice University, MS 602 6100 Main Street Houston, TX 77005 jdh(a)rice.edu / 713-348-4142 hartgerink.rice.edu

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How to Align Chromosome Models with Different Number of Atoms?
by Cardiff Jiang 30 Jul '21

30 Jul '21

Dear ChimeraX User List, How can I compare two chromosome 3D models (PDB files) that have different numbers of "atoms"? Matchmaker tool reports, "Reference and/or match model contains no nucleic or amino acid chains. Use the command-line 'align' command to superimpose small molecules/ligands." align #1 toAtoms #2 reports, "Unequal number of atoms to pair, 49 and 63." align #1 toAtoms #2 matchNumbering true reports, "Pairing dropped 49 atoms and 63 reference atoms. No atoms paired for alignment." align #1:1-40 to #2:1-40 reports, "No atoms paired for alignment." How should I compare two chromosome 3D models below? Thank you. [image: image.png] Best regards, Zichen "Cardiff" Jiang

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Change default volume display settings?
by Oliver Clarke 08 Jun '21

08 Jun '21

Hi, Is there any way in ChimeraX to change default volume display settings? For example, I would like to set all volumes to "step 1" by default - in Chimera I can set these defaults in the Volume Viewer menu but I can't see an equivalent in ChimeraX. Sort of related - I wonder if it would be possible to have the option to set default display preferences for molecules or maps? Or more generally, have a script that executes when a file of a particular type is loaded - similar to how the startup commands are executed when ChimeraX is started, but triggered by the opening of a particular filetype and applied to that particular model? Cheers Oli

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Consultation about developing plug-ins in ChimeraX
by Chen, Xiang 28 May '21

28 May '21

Dear Sir or Madam, I am a graduate student in the Department of Computer Science at the Memorial University of Newfoundland. I am currently engaged in developing and researching VR applications to visualize biological microstructures. I learned that Chimerax is a relatively mature piece of software, containing many excellent functions and features. So I'd like to know: 1. Is ChimeraX completely open-source and free? I will only use it for research and non-profit purposes. 2. If ChimeraX is open source, is there a description or summary of the structure/principles of the source code? (In order to learn what features are implemented by each code file.) 3. May I develop new plug-ins/bundles/modules based on ChimeraX's VR mode to implement one or more new features/functions? Could you please briefly describe the feasibility of developing it? Best regards, Xiang Chen --- Xiang Chen, M.Sc. # 201992538 Department of Computer Science Memorial University of Newfoundland St. John's, NL, Canada T (709) 219-2960 / E xiangc(a)mun.ca

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Structure move
by Silva, Chinthaka Mahesh 28 May '21

28 May '21

Hello, If I have more than one structure opened in ChimeraX and want to move them apart, can I do that? I see that I can move a structure model using 'right mouse' option, but not the structures. Chimera had the option to do this by deactivating a structure. Thanks! -chinthaka

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Pair-fitting in ChimeraX
by Rachael Coleman 28 May '21

28 May '21

Hello again, You guys were so helpful last time I figured I'd just ask for help again! I'm trying to do something that I know is a feature in PyMol but I'm not sure if it is a feature in ChimeraX (yet). In PyMol, there is a function to pair fit over specific atoms between two different structures. I have tried using the Matchmaker tool in ChimeraX to do this, but I think the dilemma is I'm trying to align the protein relative to the position of specific atoms in a heme cofactor across two different structures and that isn't something in the primary sequence of the protein. I also could just be doing something wrong in the matchmaker process. Do you know if there is an easy way to accomplish this in ChimeraX? Best regards, Rachael Coleman -- *Rachael E. Coleman* PhD Candidate, Lancaster Group Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853 Pronouns: She, her, hers

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