[Chimera-users] .sld (MOLCAD, Sybyl 8.0) file import or visualisation of an inner surface (of a protein) in Chimera

[Elaine Meng]

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