Hi James -
You could put in a feature
request<http://sourceforge.net/p/pymol/feature-requests/> to ask that
non-canonical residues be included in the preset.
In the meantime, the Property
Selectors<http://www.pymolwiki.org/index.php/Property_Selectors>, Single-Word
Selectors<http://www.pymolwiki.org/index.php/Single-word_Selectors>, and
Selection Algebra<http://www.pymolwiki.org/index.php/Selection_algebra>
operators and are going to be your friends here. For dashes, use the
distance<http://www.pymolwiki.org/index.php/Distance> command.
For example, the following lines will show your ligand(s) as sticks and
residues with any atom near the ligand as lines, and draw dashes for the polar
contacts between them:
###
select ligand, organic
as sticks, ligand
select binding_site, br. all within 4 of ligand
show lines, binding_site
as nb_spheres, binding_site and solvent
distance ligand_polar_conts, binding_site, ligand, cutoff=3.5, mode=2
###
Using combinations of these selectors, you can come very close to re-creating
whichever preset you wanted to use. Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Nov 6, 2014, at 3:50 AM, James Starlight
<jmsstarli...@gmail.com<mailto:jmsstarli...@gmail.com>> wrote:
Dear Pymol users!
Typically when I'm looking at the ligand binding sites (present->show of the
receptor-ligand.pdb complexes all receptors non-canonical residues or the
different titrable forms of the standard ones (e.g HIP-protonated HIS or ASH-
protonated ASN) are recognized as the ligands as well and pymol try to find
hydrogen bonds or vdv contacts of these residues with its surroundings. How I
could prevent it to see only on the ligand surrounding within such pdbs? What
another pymol options will be useful for the ligand sites visualization?
Thanks for help,
James
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