VMD-L Mailing List

From: Bob Johnson (robertjo_at_physics.upenn.edu)
Date: Tue Feb 27 2007 - 16:21:12 CST

Hello everyone,
For visualization purposes, I would like to make a volume map for each frame of
a trajectory. I do not want to combine them at the end via their average value.
How would I do this from the script level? I tried the following:

for {set i 0} {$i < $num_frames } {incr i} {

animate goto $i
volmap density [atomselect top "water"] -res 1.0 -radscale 1.0 -weight mass -mol
top

}

However, all I obtained was $num_frames volume maps of the same frame (i.e. the
frame that corresponded to the current position of the "trajectory slider" on
the VMD Main window). If I type the commands within the loop in a Console
window, everything seems to work out fine. Any suggestions on how I can do
this?
Thanks,
Bob