February 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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Commands - bond angle and minimize
by chung kelvin 02 Mar '22

02 Mar '22

Hello all and Elaine, I am new here and would greatly appreciate Elaine and the Chimera Team, ChimeraX is so wonderful and you guys are not just providing the support to scientists, but advancing drug discovery and life science for humanity. Long story short, I have 3 problems in creating an enzyme-substrate model 1. I make a bond between the substrate and the enzyme, however, I could not make a right bond angle (kindly see the attached file, the bond angle between "Ser70 OG", "UNL1 C7", and "UNL1 O2", should be 120). I tried the command "bond angle", but don't know how to use it, and could not find the description about this command. How could this command be used? Could the bond angle be changed in Chimera? 2. 3. If the bond angle can be fixed, I need to eliminate any clashes before conducting energy minimization, however, the Tool "Rotamer" could not be applied to this covalently bound ligand. Is there some way to generate "rotamer" for this case? 4. 5. In the old version Chimera, there is a Tool called "minimize structure" and "Join Model (under "Build structure")" would it be any similar Tool in ChimeraX? 6. Again, thank you very much for your help. Cheers Kelvin Chung ABCT Department The Hong Kong Polytechnic University

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Permission denied writing file...
by 翼翱张 01 Mar '22

01 Mar '22

Hi Sir/Madam, When I press the button ‘save snap shot to desk’, it shows ‘Permission denied writing file C:\Users\zhang\Desktop\image1.png’. how should I open the permission? Please help me. Looking forward to your reply. Sincerely, Wing 从 Windows 版邮件<https://go.microsoft.com/fwlink/?LinkId=550986>发送

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Re: [chimerax-users] How to view SwissDock output in ViewDockX
by Eden Fussner - Dupas 27 Feb '22

27 Feb '22

Hi Elaine, I’m not sure if you’ve answered this elsewhere - but I am having the same issue another user was having. The output of Swissdock isn’t being recognized by the ViewDockX tool. I am trying to pick the best model stearic acid in this PLAT protein (an AlphaFold model). Any help would be most appreciated. Warmly, Eden

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Stack thickness question and cine playing?
by Rubenstein, Jason 25 Feb '22

25 Feb '22

Hi! Two questions: 1. This 3D dataset is only about 30 mm thick in the Z direction. When ChimeraX is displaying it, it shows the thickness about 50x too thick. Any way to adjust this? [cid:007921ae-20a5-4928-963c-23013d90a69e] 1. this is a "4D" dataset, with 20 phases of 3D stacks. Any way to "play" the cine? Thanks! Jason Rubenstein, M.D. Codirector, Cardiac MRI Associate Professor, Medical College of Wisconsin

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