VMD-L Mailing List

From: Storr, Mark (Mark.Storr_at_nrc.ca)
Date: Tue May 14 2002 - 09:51:06 CDT

Hi,

with the following VMD provided script it is possible to make a particular
selection and for each frame of an animation dump out that selection to
separate pdb file.

set sel [atomselect top "criteria"]
set n [molinfo top get numframes]
for { set i 0 } { $i < $n } { incr i } {
  $sel frame $i
  $sel update
  $sel writepdb water_$i.pdb
}

Obviously if one has a file with a large number of frames then this approach
is somewhat prohibitive, one could change the incr i to only pick out
certain frames, but the most obvious approach would be to write a new single
dcd file which contains only the selected atoms at each frame. So I was
therefore wondering if this is possible and if so how this may be achieved.
Many Thanks

Mark