[chimerax-users] 2D Residue Plot

[Elaine Meng]

Oh, now I see that choosing the residue plot option changes the orientation of the 3D model (to best spread out the interface residues in the XY plane, I'm guessing), and then slices in 2D to give the plot.  I was checking whether the 3D matched the 2D, which it does at that point, without realizing the 3D view had been reoriented automatically.

Maybe the programmer who created the tool can comment further, but I suspect you are right that each interface is positioned with some algorithm to spread out its residues, and if the interfaces of  superimposed complexes are somewhat different, the diagram orientations may also be visibly different. 

Sorry for the inconvenience,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Mar 11, 2022, at 12:55 PM, Avinoam Aryeh Singer via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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
> 
> 
> <Screen Shot 2022-03-11 at 12.33.45 PM.png>
> 
> 
>> On Mar 11, 2022, at 11:43 AM, Avinoam Aryeh Singer via ChimeraX-users <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
>> 
>> ​<pastedImage.png>
>> 
> 
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