[chimerax-users] Selection of the organic ligand

[Elaine Meng]

Hello,
You may have to experiment with that structure interactively to figure out what commands will work.

If the part that you don't want to include is near the part that you do want to include, those two parts might be all in the same single residue. In that case it would be difficult to get only the part you want except by listing all of the atom names to deselect in that residue.

However, if they aren't all in the same single residue, here are some things you could try in the command instead of just "ligand" but I don't know if they will work on that specific structure:

ligand & ~ protein
ligand & ~ :ala,arg,asp,asn,cys,glu,gln,gly,his,ile,leu,lys,met,mse,phe,pro,ser,thr,trp,tyr,val

& means intersection, ~ means NOT, see:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#combinations>

See also definitions of  "ligand" "protein" etc.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#builtin>

Try with command "select" to see if it gets what you want, e.g.

select ligand & ~ protein

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

> On Mar 28, 2022, at 7:27 AM, Enrico Martinez via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX users!
> Normally I use the selection name "ligand" to select all atoms of the
> organic ligand. For example:
> define centroid ligand name lig_com
> 
> sometimes depending on the pdb file, this command also selects one
> residue (located in the pdb file just near the ligand), considering it
> also as a part of the ligand.. May I use another selection to
> explicitly exclude all 20 natural amino-acids from the ligand
> selection?
> Many thanks in advance!
> Enrico