VMD-L Mailing List

From: Wolf Dapp (wolf.dapp_at_googlemail.com)
Date: Fri Jun 29 2012 - 08:57:04 CDT

Hi there,

I am struggling with VMD's selection capabilities. I have several frames
of xyz data. Some atoms have different types in different frames, and I
want to reflect this in atom size (in VDW representation).

I know VMD does this not automatically (see
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/11142.html )

After long googling, I tried to include the following in my startup file:

set num [molinfo top get numframes]
set sel0 [atomselect top "name Q"]
mol selupdate 0 0 1 # **
for {set i 0} {$i < $num} {incr i} {
     animate goto $i # **
     $sel0 frame $i # **
     $sel0 update # **
     puts "frame: [$sel0 frame], particles in selection0: [$sel0 num]"
     $sel0 set radius 0.5
}

The commands marked with "# **" I tried with and without, in various
combinations.

The result is that the selection is always empty (in the initial frame,
there are no atoms of type Q). [I've tried different names as well]

I also tried using pdb input files instead of xyz files, and put a
condition in the (otherwise unused) "occupancy" field, with a boolean
comparison, also to no avail.

It seems (also from the GUI output, such as coloring by occupancy, and
labelling atoms by name) that neither occupancy nor name is updating at
all, even though "update every frame" is activated.

Is there something I am overlooking or am blatantly doing wrong? Is
there a better property to use rather than name or occupancy?

I am using "VMD for LINUX, version 1.8.7 (August 1, 2009)" on OpenSuse
11.3. Does this matter?

Thanks in advance for any pointers you can give me.

Wolf Dapp