[chimerax-users] interface residue plot save as text file?

Elaine Meng meng at cgl.ucsf.edu
Tue Jan 28 09:18:25 PST 2020


Hi Marta,
Only the plot image itself retains the layout, but if you just wanted to get a list of the residues in each interface, you could

(1) in the chain plot (the first plot, not the residues plot), 
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#diagram>

...use the edge context menu on the specific edge of interest to select the contact residues.  There are a few different choices in that menu depending on what you actually want:

• Select Contact Residues of [chain1] and [chain2] - select the chain1-chain2 interface residues of both chains
• Select Contact Residues of [chain1] with [chain2] - select the chain1-chain2 interface residues of chain1
• Select Contact Residues of [chain2] with [chain1] - select the chain1-chain2 interface residues of chain2

(2) when you have selected whichever set of residues you are interested in, write a list of their names using command:  info residues sel

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#residues>

The list is just written to the Log rather than a file, but you could then save the Log to a file, or copy text from the Log and paste it into a text file. 
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/log.html>

(3) or, if you wanted to save the selected residues as a PDB file (3D coordinates) use the “save” command with option “selectedOnly true”, for example something like:

save /Users/meng/Desktop/interface12.pdb selectedOnly true

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>

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


> On Jan 28, 2020, at 6:30 AM, Marta Perez Illana <marta.perez at cnb.csic.es> wrote:
> 
> Hi alI
> I have very recently started to play around with ChimeraX.  I am trying to use the interface functionality as a substitute of traditional find contacts/clashes ( I am aware of the differences but I think for my purpose are both fine).
> 
> I would like to save somehow the "interface residue plot", rather than the image of the plot per se, a kind of text file for example... is there a straight fordward way that am I missing?
> Thanks!!
> Marta
> 




More information about the ChimeraX-users mailing list