Hi Amna,
> i want to know i could show just the part of protein intercting with ligand
> and want to hide the rest portion of protein.the non-interacting reisues
> should not be displayed?
Next to your protein name, click A > Preset > Ligand Sites > Cartoon.
Now you can hide the protein that's non-interacting with the ligand by
hiding all protein atoms not being shown as lines, by typing:
hide everything, polymer and not rep lines
> how can show the small hydrogen bond less than 2 ?
First, disable the polar contacts from the previous step by clicking
on its name, it'll be something like "proteinName_pol_conts". Those
h-bonds should now be hidden. Next, you will need to create, by hand,
the new polar contacts object with your non-standard cutoff. The
command to locate hydrogen bonds between the visible ligands and
visible polymer less than 2.0 Angstroms is:
dist smallHbonds, vis and organic, vis and polymer, mode=2, cutoff=2.0
Now the "smallHbonds" object will have only those h-bonds < 2.0 Angstroms.
Check out the PyMOLWiki (http://pymolwiki.org/index.php/Main_Page) for
more help.
Cheers,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrödinger, Inc.
(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120
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