Re: [PyMOL] protein-ligand interaction

[Jason V. <jas...@sc...>]

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) Jas...@sc...
(o) +1 (603) 374-7120