Hi John, My guess is that that kind of image is usually made with VMD. You can create all kinds of 3D objects in ChimeraX, however, by defining them in the simple BILD format. The format is described here, with links to examples that include arrows: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html> Another way is with the "shape" command to create surface models. The advantage is that you can change their colors and easily open/close them individually afterwards, unlike the set of objects defined by opening a BILD file. However, it would be harder to define each arrow (one cylinder + one cone) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/shape.html> Either way you'd want to script it somehow, as defining them one by one would be quite tedious. There are a few other formats that can also be used to define 3D objects in ChimeraX, in case you want to take a look: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#object> 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 25, 2024, at 8:19 AM, John Watters via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi All,
I was wondering if anyone had any advice on how to make figures where vectors show the difference in the RMSD of the alpha carbons like in A/C here in ChimeraX:
From this paper: https://elifesciences.org/articles/51898
Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing Chemical modifications near the tRNA anticodon and specific mRNA–tRNA pairs combine to control the ribosomal three-nucleotide mRNA reading frame, essential for the sequential addition of amino acids into polypeptide chains. elifesciences.org