[Chimera-users] Show only molecular pocket surfaces

Tom Goddard goddard at cgl.ucsf.edu
Tue Sep 22 10:10:32 PDT 2009

Hi Natalie,

  It is unfortunately a bit tricky to show just the inner pocket surface 
of a molecule in Chimera.  Here's one way.  Create the surface then use 
the following command to make it possible to select the separate 
connected pieces of the surface:

    ac Sc

(This runs the keyboard shortcut "Sc" - split connected pieces of 
selected surface.)  Now select the outer surface with the mouse 
(ctrl-click) and use a command to delete it:

    ac Ds

(Keyboard shortcut "Ds" - delete selected surface pieces.)

  These steps that change the molecular confuse Chimera and the Actions 
/ Surface menu then doesn't work on the inner piece.  The problem is 
that the molecular surface no longer matches the atomic coordinates in 
the way Chimera expects. To get those menu entries to work delete the 
atomic model and reload another copy.  A drawback of all this is that it 
will no longer color the surface to match the atoms.


-------- Original Message --------
Subject: [Chimera-users] Thanks for the help,    Is it possible to only 
show the "inner surface"?
From: Xarana
To: chimera-users
Date: 9/22/09 2:07 AM
> Hi Elaine,
> Thank you very much for your quick help. That really helped a lot and the
> differences are small. One last question: 
> Is there a possibility to only show this "inner surface" without the outer
> one for more clarity? I have to compare in 10 different structures (NMR
> solved) the extent of this cavities. And sadly SYBYL is not able to save as
> any other file format. 
> Best wishes,
> Natalie Bordag
> PhD student
> -----Ursprüngliche Nachricht-----
> Von: Elaine Meng
> Gesendet: Montag, 21. September 2009 22:28
> An: Xarana
> Cc: chimera-users at cgl.ucsf.edu
> Betreff: Re: [Chimera-users] .sld (MOLCAD, Sybyl 8.0) file import or
> visualisation of an inner surface (of a protein) in Chimera
> Hi Natalie,
> Chimera does not know the *.sld file type.  Can SYBYL save this file  
> in a format Chimera knows, such as VRML?
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>
> If not, you could try opening the structure (PDB or Mol2 file) in  
> Chimera, instead of the surface file, and have Chimera calculate the  
> surface.
> In Chimera, you can display the surface with "Actions... Surface...  
> show".  The default in Chimera is also to use a 1.4 Angstrom probe.   
> That would generate both the inner and outer surfaces, which you could  
> see by slicing the structure in the Side View (under Favorites menu).  
> There will probably be differences in the surface due to the different  
> default atomic radii in Chimera and SYBYL, but I would not expect them  
> to be large.
> I hope this helps,
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Sep 21, 2009, at 10:34 AM, Xarana wrote:
>> Hi,
>> My interest is a 4 helix protein which has a cavity inside. A  
>> colleague generated with a 1,4 Angström probe this "inner surface"  
>> with Sybyl for me and exported the surface as .sld file. Can I  
>> import this file into chimera somehow? Alternatively, can I generate  
>> such a surface with chimera?
>> My knowledge of protein visualization is limited and I am very  
>> thankful for any help
>> Thank you very much in advance.
>> Best Wishes
>> Natalie
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