Thanks Jerome!

It worked! I also checked out your website and your tutorial in French. They're both great!

-Charlotte



From: Jerome PANSANEL <j.pansanel@pansanel.net>
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Selecting residues on surface only
Date: Wed, 11 Jan 2006 17:26:55 +0100

Hi,

Le Mercredi 11 Janvier 2006 17:27, Charlotte Habegger-Polomat a =E9crit=A0:
  
Hello Pymol users!

As a fairly unexperienced user of Pymol, I have not yet found a way to
select all residues in one of the cavities in my protein of interest.
When I render the protein as a surface, I can't select and visualize the
individual residues in the cleft.
    

You can use the clipping planes when you want to explore the core of your=20
protein (shift+right-button, move mouse up/down).
Another way is to select your ligand inside your cavity, then select around
(menu A -> around -> 6 A for your ligand selection) and then select S->=20
surface.

  
When not rendered as a surface, I=20
can't seem to select only residues on the surface and not those buried
inside.

Is there a straightforward way to do this (select and visualize the
residues on the (outside) surface of a cavity, with their labels)?
    

I publish today a pre-release of a PyMOL tutorial in french :
http://www.pansanel.net/chemistry/resources/PymolIntroduction.pdf

You can take a look !

Jerome Pansanel