May 2023 - ChimeraX-users - RBVI Mailing Lists

ChimeraX 1.6.1 release
by Eric Pettersen 10 May '23

10 May '23

UCSF ChimeraX version 1.6.1 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html <https://www.rbvi.ucsf.edu/chimerax/download.html> Updates since version 1.5 (Nov 2022) include: - ESMFold protein structure prediction and residue-residue error plot - Add Charge GUI - Dock Prep GUI to repair side chains, add hydrogens, etc. - Render by Attribute GUI for coloring by atomic or residue values - swapna command to mutate nucleic acid residues - invert chiral center - read SwissDock docking results - Blast Protein query sequence can be pasted in or specified by UniProt ID - browse/fetch medical images from The Cancer Imaging Archive - read medical images in NIfTI (.nii) and NRRD (.nnrd) formats For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog <https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog> For those of you who downloaded plain 1.6 while it was briefly available, please upgrade to 1.6.1. It has several bug fixes that 1.6 should have had but didn't. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Clipped surface coloring
by Noam Prywes 10 May '23

10 May '23

Hi all, I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity. Do I need to make a .defattr file that colors by atom instead? Best wishes, Noam [image: Screenshot 2023-05-10 at 7.42.14 AM.png]

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Question in using ChimeraX ----mesh parameters
by Wang, Shuhui 10 May '23

10 May '23

Hello developers, I have a question in using ChimeraX. May I ask how can I change the density of grids and line size of the mesh for a volume? Best, Shuhui

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Re: [chimerax-users] [Chimera-users] Utilizing Chimera in Web-Based Workflows
by Tom Goddard 10 May '23

10 May '23

Hi Rafi, You could have a Google Colab notebook install ChimeraX and then you could run ChimeraX command in nogui mode or python code through the ChimeraX REST facility, and possibly save images of the graphics to show in the notebook. But I don’t grasp the value of it since ChimeraX is all about interactive visualization where you can rotate and inspect structures. One issue you will face is that ChimeraX cannot be installed without agreeing to a license when dowloading - not sure how you might handle that in a notebook. But I suggest figuring out the valuable use case first. Tom > On Apr 21, 2023, at 5:28 AM, Zach Pearson via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Rafi, > > We are working hard to fully deprecate Chimera, and haven’t made its source code accessible for use or extension outside of the desktop application. I would caution against looking for it; the compilation process is complex and depends on resources that may not even be available anymore. Chimera was also written in Python 2.7, a language the computing community is working hard to put to rest — Colab doesn’t support it anymore! > > We do have plans to release a substantial part of ChimeraX on PyPi this year as a public beta, and I’ll make a note to send you an email when that release happens. Then you should be able to use it in Colab like any other PyPi package. Let me know if I can answer any other questions you may have. > > ------------------- > Zach Pearson > Programmer, ChimeraX Team > UCSF RBVI > zjp(a)cgl.ucsf.edu > > > >> On Apr 20, 2023, at 13:44, Rafi Brent via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >> >> To whom it may concern, >> I'm wondering if there's any way to access Chimera without having the GUI downloaded on a local computer. Specifically, I'd like to run chimera as part of a public Google Colab (.ipynb) notebook, which would allow users to access the chimera functionality through either installing a PyPi package or calls to a web-accessible API. Do you know of any tool like this, or have any other ideas for how Chimera could be used in Colab notebook? Thanks so much for any advice you may have. >> >> Sincerely, >> Rafi Brent >> _______________________________________________ >> Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu >> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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request for an example command line
by James Raymond 09 May '23

09 May '23

I am having trouble understanding the manual. I wish to show the side chain for a particular amino acid in my protein. What is the command line to do this? thank you James Raymond

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Failing to complete dimer prediction
by Tal Jeffrey 09 May '23

09 May '23

Dear all, I am trying to use ChimeraX to predict the structure of a dimer as part of my Master’s thesis. I was able to produce a model of the monomeric structure without issue have not been able to do the same for the dimer. I am currently subscribed to Colab Pro so had assumed that the 15.0GB GPU RAM would be sufficient. The structure is 1361 amino acids long but AlphaFold2 is still able to produce the first two models successfully. However, I have not been able to produce any iterations past this stage. Any guidance on how to complete the model would be much appreciated! Alternatively, I would also be glad to extract the output of the first two models (e.g. .pdb files, plDDT plots, PAE plots, MSA heatmaps) but because the prediction does not run to completion I don’t know how to access/extract these. I have really enjoyed using the program and hope to include the structure of the dimer in my thesis before I submit in three weeks’ time. Many thanks, Tal

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Map Comparisons vs Model Comparisons: Which represents differences more accurately?
by Kevin Felt 09 May '23

09 May '23

Dear Chimerax Developers, There is a debate in my lab about the best way to compare two PDBs of the same protein bound to different ligands; the goal is to identify subtle differences in the binding pocket between the ligand-bound conditions. One method of comparison is to fit the two density maps together using the FitMap function, and then fit each PDB into their respective maps which have been aligned. Another way is to simply align the two PDBs (such as the align function in Pymol). Using these two methods results in slightly different alignments of the PDBs and thus give slightly different positional differences of the binding pocket and ligands. The resolution of these density maps range from 2.4 - 3.5 angstroms. Which way would be the more accurate way to look at the differences between two similar models? Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University

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pae plot
by John Maximos [Pharma] 09 May '23

09 May '23

Dear Chimerax Team, I have a problem that the pae plot color is not adjusted like the green one. How to solve this problem? I attached here a screenshot from my laptop. Best Regards, John Maximos [cid:image003.png@01D9827F.FEF05100] www.evapharma.com<https://www.evapharma.com/>

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making movie of helical Assembly
by mailman-bounces＠cgl.ucsf.edu 08 May '23

08 May '23

From: "Sen, Anindito" <andysen(a)tamu.edu <mailto:andysen@tamu.edu>> Subject: making movie of helical Assembly Date: May 7, 2023 at 11:53:16 PM PDT To: ChimeraX-users <chimerax-users-bounces(a)cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>> Dear All, I am trying to make a movie where I can show the atomic model of the subunits appearing one after another following the helical pattern forming the filament. How can I do that? Stay safe & Regards Anindito Sen. Ph.D <>

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cannot open chimerax with structureviz (using ChimeraX 1.5 and cytoscape 3.9.1)
by ora.furman-schueler＠mail.huji.ac.il 08 May '23

08 May '23

Dear Support team We are teaching a network course and would like to show an example of analysis of proteins as networks. I have tried to follow the structureviz2 tutorial but I cannot get past the very first step of linking ChimeraX to cytoscape. I did define the Chimera location path /Applications/ChimeraX-1.5.app/Contents/MacOS What am I doing wrong? This is the error message that I get in cytocape. Launching Chimera  Launching Chimera ...  UCSF Chimera could not be launched. Make sure that the correct path to Chimera is set in structureViz -> Settings… thank you for your help! Ora Prof. Ora Schueler-Furman Dept. of Microbiology and Molecular Genetics, IMRIC Jacob Epstein Chair in Bacteriology Hebrew University, Hadassah Medical School POB 12272, Jerusalem 91120 Israel Tel: 972-2-675-7094 FAX: 972-2-675-7308 Furman lab site: www.cs.huji.ac.il/~fora

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