VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Aug 04 2007 - 08:00:48 CDT

Hi Francesco,
hiding the chloroform to see the solute should be easy enough if you
make your graphical representation
"not resname XXX" (where XXX is whatever residue name chloroform has in
your system).

When VMD reads a structure, it has several steps that it goes through to
try to assign elements to each atom. The first (and most obvious) is
that some file formats actually carry element names or numbers;
sometimes it has to fall back to guessing based on atom name, which is
probably what is going on here -- atoms named Csomething are being IDed
as carbon instead of chlorine. What type of file are you reading in to
provide the topology information for your structure? And what atom name
do your chlorine atoms have?

Best,
Peter

Francesco Pietra wrote:
> Dealing with a chloroform box from Amber9, I was unable to hide the chloroform
> molecules in order to see the solute better.
>
> Curiously, if I set to show carbon only, this is performed correctly for the
> solute molecule, while chloroform is shown as an ammonia-like
> umbrella with four identical atoms. I.e., chlorine is shown as if it were
> carbon. I was unable to trace where to deal with chlorine atom.
>
> Thanks for help
>
> francesco pietra
>
>
>
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