Hi Enrico,
I think it's because you are selecting side chains, glycine has no sidechain
and alanine has single carbon atom side chain so this representation won't work
for it. You would need to remove the sidechains from the selection to make it
apply to the backbone atoms, i.e. cmd.select('rep lines and poly)
Cheers,
Ali
On 27/1/22, 11:22 pm, "Enrico Martinez" <[email protected]> wrote:
additional question in the same field:
as I've mentioned before, before applying distance-based filtering, I
would like to change the representation of the lines to ball-and-stick
for the residues involved in the interactions:
cmd.select('rep lines and sidechain')
cmd.show_as('sticks', 'sele')
cmd.set('stick_radius', '0.10')
cmd.set('stick_ball', 'on')
cmd.set('stick_ball_ratio', '2.2')
I've just noticed that some residues remain their "line"
representation, notably for hydrophobic (Gly, Ala) residues. How could
it be fixed ?
чт, 27 янв. 2022 г. в 12:38, Enrico Martinez <[email protected]>:
>
> Thank you very much, Ali!!
> Cheers,
> Enrico
>
> чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay <[email protected]>:
> >
> > Hi Enrico,
> >
> > You need to use the byres or br. Selection
(https://protect-au.mimecast.com/s/4MzUCROND2uvY6pqpi9A9Zw?domain=pymolwiki.org)
> >
> > 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" <[email protected]> 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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