From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 06 2009 - 14:51:02 CST

hi everybody,

in the past there have been repeated requests for supporting
a varying number of atoms in VMD. while this requires some major
rewrite of the VMD code base, i have just implemented an automated
version of one of the possible workarounds, i.e. padding the
structure with atoms that are normally not shown. the majority
of people asking for this feature were using the xmol style
.xyz format, and this is the only format supported.

before adding this to VMD itself, i would like to get some
feedback on the implementation and usefulness, as well as
bug reports, if needed. the feature is implemented as an
addition to the topotools plugin and can be downloaded from:
http://sites.google.com/site/akohlmey/software/topotools

after following the installation instructions and starting
a new instance of VMD, you can read in a .xyz file by:
topo readvarxyz filename.xyz

this will automatically create a visualization with the
default settings. please note, that the visibility of an
atom is encoded into the user field by a +/- 1 value.
for efficiency reasons, atoms are sorted prior to storing
internally, so bonds may not be preserved, and the use
of a Dynamic Bonds representation needed. on that note,
all visualizations that are not supposed to show the
"invisible" atoms at (0.0,0.0,0.0) have to use "and user > 0"
as selection string and activate the "Update Selection Every Frame"
flag in the Trajectory tab of the Graphical Representations dialog.

comments are very welcome,
    axel.

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.