- ChimeraX-users - RBVI Mailing Lists

Download issue for Realsense plugin
by Casey Eubanks 12 Apr '24

12 Apr '24

Hey guys, I am trying to download the realsense plugin for Chimerax but I am getting this error on the download page [cid:image001.png@01DA8CC9.5111D810] Can you help me with this? Thanks, Casey Eubanks Service Desk Specialist MOBILE (205) 617-0581 time zone United States, Central Time Zone (CST) [cid:image002.png@01DA8CC9.5111D810]<https://www.biocryst.com/> "Go Fast, Patients are waiting" If you need immediate IT support please submit a ticket to ITsupport(a)biocryst.com<mailto:ITsupport@biocryst.com> CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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hide silhouettes for pseudobonds and mesh
by Daniel Larsson 12 Apr '24

12 Apr '24

Hi all, Is it possible to specifically hide silhouettes? The “graphics silhouettes” command unfortunately does not take a spec argument. One example is to hide it for the mesh when you want to show the model and the map at the same time. Silhouettes around the mesh can make the scene look very cluttered. For this particular case, my colleague showed me a trick to use the selection command instead of “graphics silhouettes” and change the appearance of the selection, e.g. “graphics selection color black width 1”. But it gives slighly different apperance with far clip planes, where silhouettes are truncated while selections are enclosing clipped elements, removing some of the depth illusion from the mist. Another scenario is for pseudobonds, e.g. when displaying cartoon and mainchain atoms at the same time using the trick with “cartoon suppress false; cartoon tether opacity 0” given in this thread https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… I like to have the cartoon visible to guide the eye where the main chain goes, but I do not want the pseudo bonds to be visible since that adds clutter and is confusing. But the silhouettes command will outline the connections to the ribbon for the C3’ and C4’ atoms in nucleic acids. 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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ChimeraX download for academic research
by Muhammad Tahir 12 Apr '24

12 Apr '24

Dear management Have a good day. I did not see the link for subject download please. COuld you help -- *Warm Regards:* *Dr Muhammad Tahir Khan* *PhD Bioinformatics* *YOUTH EDITORIAL BOARD MEMBERS * *Springer; Interdisciplinary Sciences: Computational Life Sciences* *https://www.springer.com/journal/12539/editors <https://www.springer.com/journal/12539/editors>* *Google Scholar: https://www.springer.com/journal/12539/editors <https://www.springer.com/journal/12539/editors>* *ORCID ID:*https://orcid.org/0000-0003-1158-2133

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chimeraX silhouette look spotty
by kellychen52071＠gmail.com 11 Apr '24

11 Apr '24

Dear ChimeraX support team, I'm experiencing an issue with ChimeraX silhouette showing dark spots. I’m using ChimeraX version 1.7.1. Please see the picture attached. Could you please help me resolve this? I’m using the latest version of macOS Sonoma 14.4.1 (graphics: intel iris plus graphics; processor: 2GHz Quad-core Intel core i5) Is this a graphic issue, this may be a ChimeraX bug for the newest version of mac as my peers who are using an older version of mac do not have this ChimeraX issue.

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chimeraX silhouette show dark spots
by Kelly Chen 11 Apr '24

11 Apr '24

Dear ChimeraX support team, I'm experiencing an issue with ChimeraX silhouette showing dark spots. I’m using ChimeraX version 1.7.1. Please see the picture attached. Could you please help me resolve this? I’m using the latest version of macOS Sonoma 14.4.1 (graphics: intel iris plus graphics; processor: 2GHz Quad-core Intel core i5) Is this a graphic issue? This could be a ChimeraX bug for the newest version of mac as my peers who are using an older version of mac do not have this ChimeraX issue. Thank you for your help, Kelly

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Mesh settings in ChimeraX
by Matthew Hancock 11 Apr '24

11 Apr '24

Hello, I have a density map I am visualizing as a mesh in ChimeraX. If I recall there are settings to manipulate the mesh visualization (line width, antialiasing, etc.) but I cannot them. If they exist, where might I find them? Thank you. Best Matthew

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Dealing with netcdf trajectories
by Enrico Martinez 11 Apr '24

11 Apr '24

Dear Chimera-X users ! Typically having loaded pdb of the system I use the following command to load the netcdf file, which replaces current pdb with the trajectory: open ./trajectory_part1.nc structureModel #1 would it be possible to load in the same section the second part of the same trajectory and merge the both into the same ensemble ? E.g. if I run subsequently the same command with another trajectory, it will produce another ensemble related to the second trajectory (and not merge the both together): open ./stripped_*part2.nc structureModel #1 Many thanks in advance! Enrico

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Not able to sign up to start a thread in RBVI mailing list
by Kelly Chen 10 Apr '24

10 Apr '24

Hi, I signed up using my email address, but I don’t receive an email confirmation in the inbox with steps for finishing an account creation. I checked my spam folder as well. Could you please help me sign up an account? Thank you, Kelly

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Central path for bundles on shared computing environment?
by Ricardo Righetto 09 Apr '24

09 Apr '24

Hi, We are setting up a new cluster at our university, and I stumbled upon the following problem: our nodes used for remote visualization don't have access to the internet. Therefore, users running an interactive graphical session won't be able to install bundles by themselves, which was the case in our old cluster. One workaround is to start ChimeraX either without GUI or with X forwarding over SSH on one of the normal login nodes (no high-end visualization capability) just for the purpose of downloading and installing bundles from the toolshed. This is however inconvenient to most users. Another approach is to install using the 'toolshed' command with a pre-downloaded wheel, but also not ideal. My thought would be to preinstall the most common plugins we use (like ArtiaX and ISOLDE) into a shared location, and ChimeraX would then find the bundles installed there upon startup. Therefore, my question is: is any other path other than the user's home folder supported for installing bundles? If yes, what is the order of search paths? Alternatively, is there some environment variable or other setting that I can use to tell ChimeraX where to find installed bundles? Thanks in advance, -- Ricardo Diogo Righetto

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Morphing Protein/NA Complex
by Shawn Rumrill 09 Apr '24

09 Apr '24

Hello All, I am trying to create an animation morphing between two states of a protein/nucleic acid complex (one binary, one with an incoming nucleotide). Excluding the nucleotide, the corresponding chain IDs between structures are the same and the sequences are the same. In both ChimeraX and PyMol, I am able to create the morphing animation however, only the protein appears (nucleic acid just does not appear in the animation). Am I missing something obvious? I appreciate any insights. Thanks, Shawn R

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