Re: [PyMOL] Ligand surface

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

Hi Peter,

In order to do this you either need to extract the ligand to its own
object or unset the ignore flag on "rep surface".  That is,

# fetch the protein

fetch 1rg7, async=0

# show surface
show surface, resn MTX

# do not ignore surfacing of ligands

flag ignore, not rep surface

# force PyMOL to rebuild the surface

rebuild

Cheers,

-- Jason

On Sat, Apr 2, 2011 at 12:22 PM, Peter C. Kahn <ka...@ae...> wrote:
> Dear All,
>
>     Is there a way to show the surface of a ligand?  In the file 1RG7
> dihydrofolate reductase has the inhibitor methotrexate bound in the
> active site.  S surface yields the surface of the protein but not of the
> inhibitor, which remains as lines. The command 'select MTX, resn MTX'
> followed by S spheres for the MTX selection yields the van der Waals
> representation.  How can I show the solvent accessible surface of the
> inhibitor?
>
>     (It is easier to see the problem if you color the whole protein one
> color, e.g. magenta, and then color the methotrexate yellow.)
>
>     Is this a general problem for ligands?
>
> Thanks,
>
> --
> Peter C. Kahn, Ph.D.
> Professor of Biochemistry
> Department of Biochemistry&  Microbiology
> Rutgers University
> 76 Lipman Drive
> New Brunswick, NJ 08901
>
> Telephone:  732-932-9255, ext. 120
> Telefax:    732-932-8965
> Email:      ka...@ae...
>
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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