RE: [PyMOL] molecular surface colored by hydrophobicity

2004-02-19 Thread Warren DeLano 
Rongjin,

PyMOL can certainly color surfaces by atom color and other properties.

   show surface
   color green, elem c
   color violet, elem n+o 

But Grasp's hydrophobicity function may be doing something more
sophisticated then that...

Cheers,
Warren


 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 gu...@umbi.umd.edu
 Sent: Wednesday, February 18, 2004 7:12 PM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] molecular surface colored by hydrophobicity
 
 Dear all,
 I am preparing a figure of a molecualr surface, colored by 
 the hydrophobicity of surface residues. Can pymol do this job? 
 How about showing atom C* in a color, and N* and O* in another color?
 
 In fact I have tried GRASP but failed in coloring the 
 surface. I used r=hyd, but could not color the surface of 
 those redisues. This is an old version of grasp (1.0?). I am 
 not familiar with this program. If anybody can tell me the 
 correct way of doing it in grasp, it will also be greatly appreciated.
 
 Rongjin Guan
 
 
 
 
 
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[PyMOL] molecular surface colored by hydrophobicity

2004-02-18 Thread guanr 
Dear all,
I am preparing a figure of a molecualr surface, colored by the 
hydrophobicity of surface residues. Can pymol do this job? 
How about showing atom C* in a color, and N* and O* in another
color?

In fact I have tried GRASP but failed in coloring the surface. I used
r=hyd, but could not color the surface of those redisues. This is
an old version of grasp (1.0?). I am not familiar with this program. If
anybody can tell me the correct way of doing it in grasp, it will
also be greatly appreciated.

Rongjin Guan