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@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