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://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 > > > > > > _______________________________________________ > > PyMOL-users mailing list > > Archives: > > https://protect-au.mimecast.com/s/utRJClx1Nji2GrWxqIGRZsc?domain=mail-archive.com > > Unsubscribe: > > https://protect-au.mimecast.com/s/XwNECmO5glujXxVzLuOSHPJ?domain=sourceforge.net > > > > _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
