[Chimera-users] You are the best, that helped a lot. Thank you so much.

Natalie Bordag nataliebordag at gmx.de
Tue Sep 22 11:53:34 PDT 2009

-----Ursprüngliche Nachricht-----
Von: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Gesendet: Dienstag, 22. September 2009 20:23
An: Xarana
Cc: chimera-users at cgl.ucsf.edu
Betreff: Re: [Chimera-users] Thanks for the help, Is it possible to only
show the "inner surface"?

Hi Natalie,
If the inner surface is totally disconnected from the outer surface  
(like an inside "bubble"), it is fairly easy:

- Ctrl-click to select the surface
- use command: ac Sc
(this makes the disconnected parts into separate "surface pieces"  
that can be controlled separately; choose "Favorites... Command Line"  
from the menu to get the command line)
- Ctrl-click empty space to clear selection
- Ctrl-click outer surface to select it (now the inner surface will  
not be selected)
- choose "Actions... Inspect" from the menu to open the Selection  
Inspector.  In that dialog, Inspect "Surface Piece" and set  
"displayed" to "false."  That will undisplay the outer surface,  
leaving the inner surface.  If there are other pieces to turn off,  
repeat by selecting them and using the Selection Inspector to  
undisplay them.

If inner and outer surfaces are connected, however, it may be  
difficult to just show the part you want.  You can select sets of  
atoms and use "Actions.... Surface... hide/show" to hide or show  
their surface patches, but the problem is that it can be hard to  
figure out which atoms go with which surface patches, and some atoms  
might even form parts of both the inner and outer surfaces.

A third possibility is to use the Surface Zone tool (under Tools...  
Surface/Binding Analysis).  In that case you would need to put some  
atom in the middle of the inner surface, select it, and then use some  
cutoff from that atom.  You can add a single atom with Build  
Structure (under Tools... Structure Editing), Add Atoms section,  
"atom" (make sure to put atom in a "new model") and then move it  
relative to your first structure by checking/unchecking the boxes  
under the Command Line and using the mouse.  It can be hard to get  
the atom where you want it, and even if that part is successful, it  
may work very well either if a spherical cutoff does not separate the  
inner and outer surfaces.

The "Structure Analysis and Comparison" tutorial includes showing  
just the surface of a binding pocket:

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 22, 2009, at 2:07 AM, Xarana wrote:

> 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
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