November 2020 - 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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Bottleneck Large Surfaces
by Anderson, Jacob 04 Jan '21

04 Jan '21

With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay? ~jacob

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Change AltGr
by Daniel Esteban Palma Igor 09 Dec '20

09 Dec '20

Hi, pressing AltGr takes the cursor to the command line, is there any way to change this key? I can't write some characters when the ipython shell is docked. Regards, Daniel Palma Igor

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multiple isosurfaces for one map
by Daniel Larsson 07 Dec '20

07 Dec '20

Is it possible to visualize two surfaces for the same model? I was thinking for example for the purpose of showing two different levels of a map with the lower one as a semi-transparent surface. The work-around is to load the same map twice into two different models, but that will take up more memory and is more cumbersome. Regards, Daniel 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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New color picker alpha channel and custom color
by Daniel Asarnow 30 Nov '20

30 Nov '20

I noticed in a recent ChimeraX build the color picker has been simplified: [image: image.png] It seems we can still set the alpha channel within the "custom" color dialog, but the default color there is some shade of red regardless of the currently selected color. Could the custom dialog start at the current color by default? Setting the alpha channel via the picker is the fewest number of clicks, and starting at the current color will make slight adjustments much easier as well. Best, -da

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Problem with C2 symmetric assemblies
by Y. Mutum 30 Nov '20

30 Nov '20

Hi I have a a C2-symmetric pdb: 1be3 and have created a symmetric assembly using the command. >>> sym #1 assembly 2 newModel false The idea is to superimpose Chain /C of 1be3 and its symmetry partner with that of 3cx5 (corresponding chains -C and N) to get of deviations b/w the chains. However, when I try to 'match #1/C with #2/C, then I am getting only half of the C2 symmetric assembly superimposed. Is there a way to superimpose both of the chains-C of 1be3 to 3cx5? I could open the model 1be3 twice and then superimpose to the equivalent subunits (chains C and N) of 3cx5, one at a time. But the resulting superimposed assembly 1be3 (from 2 different models) is not going to be the C2 symmetric. In short, for 1be3: pdb, is it possible to rename the symmetry mate with different chains and get the C2 symmetric assembly as a single model? Say, for this new 1be3 C2-symetric assembly, you rename the second symmetry partners chains - Chain C as C1, Chain B as B1 for example in that new model. The idea is to have a C2 symmetric model with different chains, so that it can be compared with other models easily. Thanks Yaikhomba

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User defined color values for each residue/position
by Niccolò Arecco 30 Nov '20

30 Nov '20

Hi, I’m using ChimeraX to visualise the structure of a complex of 4 proteins. I generated a sequence alignment of protein sequences of 1 of the 4 proteins and at each column (amino acid) of the multi protein alignment I assign a score from 0 to 1, where 0 represents no sequence conservation and 1 represent perfect sequence conservation. I’d like to colour-code these values on a publicly available structure. Can I do it with ChimeraX? I tried to google a bit and read the docs but couldn’t fine a way. The input “colouring” file could be something like this tab delimited file: #POS AA SCORE 1 M 0.2 2 V 0.5 …. n N 0.8 But I can reshape it in a better format if necessary. If this is not possible to do it with ChimeraX are you aware of any other tool / software that would allow me to do this? In the end I’d like to be able to do something like ConSurf (https://consurf.tau.ac.il <https://consurf.tau.ac.il/>) does but I’d like to avoid if possible always having to use the web interface as I’d like to semi-automatise this process for every protein in the complex at least. Thanks a lot! Best wishes Nicco

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