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

On Mar 11, 2022, at 11:43 AM, Avinoam Aryeh Singer via ChimeraX-users <chimerax-users@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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