[chimerax-users] 2D Residue Plot

[Avinoam Aryeh Singer]

Hi Elaine,

I appreciate the quick response. I think that the orientation of the 2D slice is invariant, since rotating the 3D model produces the same 2D plot. The proteins are nearly identical, but slice depth is an interesting aspect that I hadn't considered. I was mostly wondering whether there's an option that gives me more control over the 2D plot, but I'm sensing that there is not.

Best,
Avi?

________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Friday, March 11, 2022 3:40 PM
To: Avinoam Aryeh Singer
Cc: chimerax-users at cgl.ucsf.edu; Fiona Aguilar
Subject: Re: [chimerax-users] 2D Residue Plot

Hi Avi,
As I understand it, the orientation is exactly a 2D slice of the current position and thus, superimposed complexes should be shown in the comparable positions.  Could it be that it is just difficult to tell because of the slightly different shapes of your proteins at the slice position? It is possible that the slice is taken at slightly different depths if the set of interface residues is a little different.

I could not reproduce the problem.  I tested by opening two similar complexes, superimposing them, using the "interfaces" command on each to get a chain diagram, and then using the edge context menu of the chain diagram to get the residue plots, see attached.  However, probably my two complexes are more similar to each other than your two complexes.

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#residue-plot>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


[cid:9BD4D92B-F2D0-4777-8FB7-D57A8EDA156B]


On Mar 11, 2022, at 11:43 AM, Avinoam Aryeh Singer via ChimeraX-users <chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at cgl.ucsf.edu>> wrote:

Hey there,

I was wondering whether there was a way to control the angle of the 2D residue plot generated from the "Interfaces" tool, such that creating plots from two aligned proteins will give me comparable plots. As you can see in the image below, the two structures are slightly rotated relative to one another, despite being aligned.

Thanks!

Avi Singer

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