Question about Creating/Displaying Vectors
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: [https://iiif.elifesciences.org/lax/51898%2Felife-51898-fig3-v2.tif/full/617,...] From this paper: https://elifesciences.org/articles/51898 [https://elifesciences.org/assets/images/social/icon-600x600@1.52e87ee6.png]<https://elifesciences.org/articles/51898> Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon–anticodon pairing<https://elifesciences.org/articles/51898> 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
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
Hi John, Here's an example using the ChimeraX shape command to draw cones from the P atoms in one RNA conformation to the P atoms in another conformation. First I show just models 5 and 7 of an NMR ensemble of an RNA hairpin, only showing the bacbkone as a ribbon open 17ra hide #1 models,atoms show #1.5 #1.7 models To show a cone between P atoms in the two conformations of residue 2 shape cone fromPoint #1.5:2@P toPoint #1.7:2@P radius .5 color blue and to show those cones for residues 2 through 21 perframe "shape cone fromPoint #1.5:$1@P toPoint #1.7:$1@P radius .5 color blue" range 2,21 This makes a separate ChimeraX model for each cone so it may run into trouble if you need 1000 arrows. Tom
On Jul 25, 2024, at 8:54 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
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participants (3)
-
Elaine Meng -
John Watters -
Tom Goddard