Wulf,
suppose you have this scenario:
Protein in chain A
Ligand in chain I
Then
create b-site, byres chain A within 5 of chain I
show sticks, chain I
show surface, b-site
should get you close.
HTH
Carsten
BTW If you replace the "create" command with "select" your surface will be
"scribed" i.e. with frizzled ends. If this is what you want then you should use
select.
-----Original Message-----
From: Wulf Blankenfeldt [mailto:wulf.blankenfe...@mpi-dortmund.mpg.de]
Sent: Wednesday, March 25, 2009 1:31 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Showing only part of a surface around a ligand
Hi all,
this question may be resolvable by sufficient RTFMing, but maybe there
is someone out there to help me...
I am trying to generate a figure in which I want to show only a part of
the protein surface around a ligand - pretty much like
preset --> ligand sites --> solid surface
I have already tried some amateur solutions like splitting the ligand
into parts, placing waters to generate pseudo-ligand atoms and the like.
Somewhat unsatisfying. I have also realized that I can click on every
atom of the protein and do a show surface, but this will drive me insane
sooner than later.
I guess it must be doable through some magic selection commands - if I
could only see how the preset command works, I could probably work it
out from there.
Can somebody please point me in the right direction?
Thanks in advance,
Wulf
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