April 2024 - ChimeraX-users - RBVI Mailing Lists

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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Opening chimera within MS powerpoint
by Prathvi Singh 09 Apr '24

09 Apr '24

Hi Elaine, I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)? This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation. Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Transparency of cartoon and surface
by Enrico Martinez 09 Apr '24

09 Apr '24

Dear ChimeraX users, I am trying to add transparency on the cartoon representation of the protein that have additionally transparent surface in the same session. hide protein target a surface protein rainbow protein target c palette paired-12 rainbow protein target s palette paired-12 transparency 90 transparency protein 10 target c The last command hides all cartoons. I've also tried adding the transparency option directly to the rainbow command: rainbow protein target c palette paired-12 transparency 20 But it had the same effect as the total disappearance of the cartoons. Is it possible to have two different levels of the transparency on both cartoon and surface representation ? Thank you in advance ! Enrico

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About surface representation
by Enrico Martinez 08 Apr '24

08 Apr '24

Dear ChimeraX users! I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation. 1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ? 2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using # first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80 This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ? Thank you very much in advance Best regards Enrico

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Suggestions for optimizing movie quality when working with file size limits?
by Vorländer,Matthias Kopano 08 Apr '24

08 Apr '24

Dear ChimeraX team, Making movies in ChimeraX is my favorite way of communicating my research, but unfortunately many journals have strict file size limits for supplementary movie files (30 MB in my case). I am wondering if there are suggestions for settings that give relatively small files with good visual appearance, i.e a specific format that works better then others. I am currently encoding in .mp4. Is it preferable to set qscale rather than quality/bitrate? I assume both bitrate and the windowsize scale linear with data size? Or are there recommendations for external software that efficiently compresses high-quality ChimeraX movies? Many thanks, Matthias

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ChimeraX-users April 2024