Hello, In addition to Elaine's pointers, you will find more examples here: https://rbvi.github.io/chimerax-recipes/ And some more, from my own work, here: https://github.com/Guillawme/chimerax-viz I try to update this whenever I produce new visualizations, so you might want to check back from time to time. I hope this helps, Guillaume ________________________________ From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Sunday, July 21, 2024 5:48:07 PM To: Gupta, Arun Cc: ChimeraX-users@cgl.ucsf.edu Subject: [chimerax-users] Re: ChimeraX journal-quality figures script ! Dear Arun Gupta, We have several examples on the website that include links to the image setup scripts (.cxc files), see <https://www.rbvi.ucsf.edu/chimerax/gallery.html> <https://www.rbvi.ucsf.edu/chimerax/features.html> ...as well as several tutorials, which may be a good idea if you want to learn how to use ChimeraX: <https://www.rbvi.ucsf.edu/chimerax/tutorials.html> As for the images you sent, they look fairly simple, just ribbons with white backgrounds and black outlines. Some sidechains are shown as sticks and others as ball and stick, and of course you can choose any colors that you want. You could do all this even not using commands, just by using the icons across the top in the Graphics and Molecule Display tabs, and selecting certain residues and using the Actions menu to change which ones are shown and their display styles and colors. See the User Guide for explanation of all these: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/toolbar.html> <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html> If you use the single-click icons, it will show the commands in the Log so that you can learn the commands. I will also give example commands below. Of course you have to modify for your own specific data (what residue numbers, what chains, what colors you want, etc.). open 2gbp open 2fw0 mm #2 to #1 set bgColor white graphics silhouettes true hide atoms color #2 purple color #1 green yellow show #1 & ligand color ligand byelement style ligand ball select #1 & protein & ligand :<4 show sel ~sel Here's a chart of named colors, but you can use basically any color you want by giving hex codes, etc. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin> There are many, many other things you can try like different kind of lighting. It is easy, just try the lighting icons in the Home or Graphics tab of the toolbar across the top. Explanations in the toolbar link above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 21, 2024, at 6:20 AM, Gupta, Arun via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX team, Recently, I came across this review article “Front. Microbiol.13, 2022, 891610” and I am quite fascinated by the visually appealing figures made in the above-mentioned review article. Since the figures were created with UCSF ChimeraX in the review article. I was just wondering can somebody advice or suggest what should be the specific ChimeraX command scripts for making similar journal-quality figures. Find attached one of the example figures from the review article for the reference. Thanks! Arun <Fig9, Front. Microbiol.13, 2022, 891610.png>l.ucsf.edu/
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