From: Axel Kohlmeyer (
Date: Sat Aug 04 2007 - 11:38:10 CDT

On Sat, 4 Aug 2007, Francesco Pietra wrote:


you can change the color assignments in the color menu.
by default VMD assumes, that all names starting with C
are carbons. since VMD has its heritage in visualizing
proteins, you will hopefully understand this choice (same
as for the 'carbon' macro).

to elaborate a little on peter's remarks. please keep in
mind, that VMD has no intrinsic knowledge of what element
a certain atom name or type is. in classical MD everything
can be everything (e.g. is an atom with mass 16 an oxygen
or a united atom deuterated methylene group?). some
molfile plugins try educated guesses on elements, but
in the end only if you use a file format that provides
the element information (fully standard conformant .pdb
files do that for example, however most programs don't
write fully standard conformant .pdb files) and if the
VMD molfile plugin reads this information, you can trust
the element information/visualization (but there currently
is no flag indicating, where the element information came
from and how much it can be trusted).

there have been discussions amongs VMD developers/hackers
on how to make the educated guesses more educated and more
consistent, but so far we only had to conclude that
consistency is not easy to achieve and what may be a reasonable
choice for one application, may make no sense for another.


FP> In summary, what remains open, is distinguishing by color chloroform from
FP> carbon, although the "type' command shows where chlorines are.
FP> Regards
FP> francesco

Axel Kohlmeyer
   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.