[chimerax-users] Interface residue selection - command line option?

[Elaine Meng]

One general note about "interfaces" (and "measure buriedArea") is to be aware that specification by chain ID will include waters, ligands, etc. with that chain ID.  If you don't want the nonpolymer parts to contribute to the buried area calculations, you need to include something like "& protein" in the atom specification (intersect with protein), or delete those atoms beforehand.

For example, 1zik has chains A and B, each with peptide and some water molecules.  It's easy to be unaware of the water molecules since they aren't shown by default.

Elaine

> On Sep 15, 2021, at 12:03 PM, Tom Goddard via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Matthias,
> 
>   I added an "interfaces select" command to select the contacting residues using buried areas to judge contacts, for example,
> 
> open 7mjs
> interfaces select /X contacting /H
> interfaces select /X contacting /H both true
> close
> 
> open 1a3n
> inter sel /A,B contacting /C,D
> 
> More details here
> 
> 	https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5232
> 
> It will be in tonight's daily build.
> 
> 	Tom
> 
>> On Sep 15, 2021, at 8:44 AM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>> 
>> Hi Matthias,
>> The "interfaces" command uses a multistep procedure of calculating buried SASA between each pair of chains and then using an area cutoff to identify which residues are involved in each interface.  
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html#interface-residues>
>> 
>> You could do it with a series of "measure buriedarea" commands, one for each pairwise combination of chains.  You would want to use the options to select residues with buried area greater than some cutoff value.
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea>
>> 
>> An alternative approach is to use "contacts" instead of "measure buriedarea" for each pairwise combination of chains.  Instead of buried area, this goes by distance between the VDW surfaces of the atoms ("overlap" is 0 where VDW surfaces would exactly touch, -1.0 where they are 1A apart, +1.0 where they would intersect by 1A).  The reason we use overlap instead of merely distance is that it accounts for different sizes of different atoms.  However it also has an option to ignore sizes and use center-center distance if that's what you want.
>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Sep 15, 2021, at 6:34 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Dear ChimeraX team, 
>>> 
>>> I am trying to selected interface residues using the “interface” tool. While doing this through the context menu of the interface plot works, I am analyzing a larger number of PDBs and am therefore looking for a way to achieve this through the command line (the contacting chains are displayed already in the log window. Essentially I wonder if it is possible to expand this to the contacting residues).
>>> 
>>> Thanks a lot in advcance,
>>> Matthias
>> 
>> 
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