January 2022 - 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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Aligning volumes without resampling - Saving a map relative to another
by Helge Paternoga 17 Mar '22

17 Mar '22

Hi, I would like to know if it is possible to save a .mrc map relative to another one. Basically, I would like to superpose two volumes and compare them outside of ChimeraX (i. e. using Coot) without resampling in ChimeraX, as it is my understanding that resampling changes the volume in question. I noticed that "fitmap" outputs the rotation etc. in the log, but I do not know if and how I can apply this to a map. Many thanks in advance, Helge

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Next/previous buttons?
by Oliver Clarke 07 Feb '22

07 Feb '22

Hi, The Next/Previous buttons in original Chimera, combined with the capacity to lock the display status of one model (using the "Skip") checkboxes, are really useful when comparing multiple maps (particularly multiple aligned maps with a single atomic model), and I really miss this functionality in ChimeraX... would it be possible to add it to the (diminishing!) list of features to port over? Cheers Oli PS My mind was blown yesterday when I found out that ChimeraX has (universal?) undo/redo bound to hotkeys! Would it be possible to add the option of user defined hotkeys...? E.g. for invoking a custom function, style, lighting etc?

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Automate calculation and saving of residues' structural attributes
by André 04 Feb '22

04 Feb '22

Hello! I'm working on an automated pipeline (in Python) for the structural analysis of proteins. In particular, I'm using Chimera to calculate and save to .txt files some structural properties of residues (namely: areaSAS, areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the inputs of the pipeline. However, currently the files are exported manually, and, for the purpose of building a fully automated pipeline, it would be great to also automate this step of calculating the attributes and exporting their respective files. I searched a lot, and tried some ways to achieve such an automation (using Chimera), but nothing worked. And I also considered using ChimeraX. In particular, I went through ChimeraX Programming Manual ( https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html#) but, if I understood correctly, I'd only be able to import chimerax and use its functions in the Python interpreter within ChimeraX (Tools >> General >> Shell). At first, I'd like to import chimerax as a module in a Python interpreter outside of ChimeraX, so that manually opening ChimeraX wouldn't be necessary in order to save the files with the residues' attributes. But, from some other threads in the mailing list, I found that it wouldn't be possible (right?) But I also found out that I could write a .py script which calculates and exports the files with the residues' properties, and then run it with ChimeraX application from the command-line, something like: *chimerax --nogui myscript.py* If that works, I think that my automation problem would be solved! The only problem is that I really couldn't figure out the Python code to calculate and export the aforementioned residues' properties (I took a look in ChimeraX Recipes (https://rbvi.github.io/chimerax-recipes/) but I couldn't find what I need, nor more detailed documentation). Given that, I'd like to know if anyone has done something like this, and/or have any guidance on how I could proceed. I really appreciate any help you can provide! (And thanks to Tom Goddard for suggesting moving the discussion here to the ChimeraX mailing list). Thank you so much, André.

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hbonds and the number of detected interactions
by Enrico Martinez 31 Jan '22

31 Jan '22

Dear ChimeraX users! I have a question regarding calculations of the hydrogen bonds and its visualisation using hbonds. Here is my command: hbonds #1 & ligand reveal true log true radius 0.06 dashes 6 color turquoise distSlop 0.4 angleSlop 20 intraRes false So I ignore intraRes (since the ligand is also present in the #1) and calculate hydrogen bonds using default parameters. 1) How can I modify geometric criteria for the calculations (is this distSlop / angleSlop) to increase the distance for the consideration of potential h-bonds ? In particular as you may see on the attached image the bond between the side-chain of the Glu166 and NH of the ligand is absent (I've just checked the same structure using py*ol and it could detect this contact). 2) In the case of another ligand, I could visualize two h-bonds provided by two hydrogens of the side chain of the Gln189 (same residue) with two different oxygens of the ligand. Is this correct? Many thanks for the tips! Yours sincerely Enrico

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ChimeraX 1.4 Download?
by Nayla Abney 27 Jan '22

27 Jan '22

Good evening, Hope you are doing well! I am trying to use your ChimeraX 1.4 download after watching this AlphaFold Protein Complex via ChimeraX Youtube video (https://www.youtube.com/watch?v=6lXeCPuTePs) However, I am having issues finding the download for the 1.4 version because your website only shows the 1.3 download (https://www.rbvi.ucsf.edu/chimerax/download.html) When I try using this version, I am having issues with inputting the sequence in the correct format because I keep getting a sequence argument error. I have tried looking up documentation for this version and this error, however, I am only seeing 1.4 documentation. Could you guide me in the right direction of where I should go ideally for the 1.4 download? I guess my Googling skills could use some help :) Thank you! ------------------------------------------------------ Nayla

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