Hi Enrico,
You need to use the byres or br. Selection
(https://pymolwiki.org/index.php/Selection_Algebra)
I.e:
cmd.select('br. (rep sticks & visible beyond 4 of not polymer)')
Also, consider hiding all protein residues and showing only the ones near the
protein, i.e.:
cmd.show('sticks','br. poly within 4 of resn XXX')
^ Where 4 is the distance and XXX should be substituted with the residue name
of the ligand
Cheers,
Ali
On 27/1/22, 10:12 pm, "Enrico Martinez" <jmsstarli...@gmail.com> wrote:
Dear Pymol Users!
I am working on the visualization of the protein-ligand contacts
identified using
preset.ligand_cartoon('pdb',_self=cmd)
Since the command also displays some residues, which are not involved
in the interactions (with the radicals located too far away) with the
ligand, I need to filter the displayed side-chains focusing only on
the important interactions. I am using a distance-based criterion for
the selection of the residues which I am going to hide.
this is what I've already tried:
# display visible side chains as the sticks
cmd.select('rep lines and visible and sidechain')
cmd.show('sticks', 'sele')
# select all visible sticks of the sidechains far away from the ligand
cmd.select('sidechain & (rep sticks & visible beyond 4 of not polymer)')
cmd.hide('everything', 'sele')
the problem is that the "select" command with such syntax, always
selects the ATOMS, but not the whole side-chains. Is it possible to
hide the whole side-chain using such syntax as well as it's displayed
label?
Many thanks in advance!
Enrico
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