You are right, thank you!
Cheers,
Enrico
чт, 27 янв. 2022 г. в 13:32, Ali Saad Kusay <akus8...@uni.sydney.edu.au>:
>
> 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" <jmsstarli...@gmail.com> 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 <jmsstarli...@gmail.com>:
> >
> > Thank you very much, Ali!!
> > Cheers,
> > Enrico
> >
> > чт, 27 янв. 2022 г. в 12:20, Ali Saad Kusay
> <akus8...@uni.sydney.edu.au>:
> > >
> > > 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" <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
> > >
> > >
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > Archives:
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> > >
> > >
>
>
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