VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jan 06 2009 - 12:30:19 CST

On Tue, 6 Jan 2009, jfgaff_at_ncsu.edu wrote:

JG> Dear all,

dear john,

JG> I have ran into a representation problem which hopefully someone can help
JG> me with. I've inserted a 4-bromophenol residue into my protein and wish to
JG> render an image. The problem is that bromine is by default white, so the
JG> color of the bond between the carbon and bromine is cyan-white. I need
JG> this bond to be colored cyan-tan, but not sure as to how to do this. I've

you go to the color menu and change the color for the atom name.
some atom names are predefined, others only show up once they
are used.

JG> tried stacking multiple representations but cannot obtain anything better

when stacking multiple representations, you have to make sure that
they are of different size or that you adjust the selection. if you
use multiple object of the same size they may show up in differently
depending on the renderer, i.e. what OpenGL displays may not be what
you'd get with Tachyon or povray.

JG> then a carbon-bromine bond to appear all tan, not cyan-tan. Any
JG> suggestions?

if you still have troubles, perhaps attaching a (small) jpeg snapshot
for illustration may help.

cheers,
  axel.

JG>
JG> Cheers!
JG> John
JG>
JG>
JG>
JG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.