Ravindranath Singh Rathore wrote:
> I am trying to display molecular surface of a protein and color
> its hydrophobic residues on the surface.
> does any one have an idea, how to do it in GRASP or in any other surface
> representation program. Thanks.
>> Rathore, RNS
> Univ. Texas Medical Branch,
> Galveston, Texas
>> ---
Hi,
well you have to generate a molecular or accessible surface ( BUILD,
Molecular surface for instance ) and then
I would color all atoms of hydrophobic residues say yellow: c=7,
r=hydrophobic
This does not alter the surface- this is done with vc=a. There may be a
simpler way but this works. You can extend this to include polar, basic etc
residues in much the same way.
For publication quality images you can write out the grasp surface and
render it with pov4grasp. Very nice pictures.
Another program I can recommend is SPOCK ( Jon A. Christopher ). Syntax is
similar to grasp.
Also vmd ( with or without msms ) works well and is possibly even easier to
use.
I had no luck with swiss pdb viewer. But it could have been just my lack of
experience with this program.
If you need more details about any of the programs I mentioned let me know.
Hope this helps.
Lothar.
--
Dr. Lothar Esser
NIH / NCI
Tel. 301-435-6163
email lesser at helix.nih.gov
