[PyMOL] odd surface appearance

[Patrick L. <pat...@dr...>]

Hi,

I sent this on New Year's Day, but didn't get much response (hung  
over?). Let me try your patience and ask again.

I'm imaging the surface of a buried pocket within a protein. The  
surface invariably has a mottled appearance, with some sections  
having distinctly different coloring than others.  An example is  
shown here (the arrows point out regions of aberrant color):

http://picasaweb.google.com/lh/photo/zQAw8C8t3sL-sbHzwIk7sQ? 
feat=directlink

I don't know why this is occurring, so it's hard to attack it  
rationally; but I can report that I have played with a lot of  
variables that seem related to surfaces, and while I can change the  
size and shape of the aberrant areas, I haven't succeeded in making  
them go away. Someone kindly suggested it might have to do with  
hydrogens being present in the file, but there are no hydrogens in  
these files.  Any suggestions welcome.

Best wishes for a happy and productive New Year.

Cheers,

Pat

------------------------------------------------------------------------ 
---------------
Patrick J. Loll, Ph. D.                  		
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pat...@dr...