[Chimera-users] Thanks for the help, Is it possible to only show the "inner surface"?

Xarana xarana at gmx.net
Tue Sep 22 02:07:12 PDT 2009

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 [mailto:meng at cgl.ucsf.edu] 
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?

If not, you could try opening the structure (PDB or Mol2 file) in  
Chimera, instead of the surface file, and have Chimera calculate the  

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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