From: Pawel Siuda (siuda.pawel_at_gmail.com)
Date: Mon Nov 26 2012 - 15:41:15 CST

Hi all,

I am trying to visualise a trajectory in which for every frame number of
molecules of interest is changing. I have used beta field in pdb file to
store a descriptor for every molecule in the system and I am trying to use
it to visualise molecules of interest. However, seems like VMD is not
updating values of beta field every frame.

I was using GUI (graphics>representations>selected atoms) to try to
visualise atoms with specified value of the beta field and I have checked
the 'update selection every frame ' button. I was also trying to use tcl
scripts (utilizing atomselect macros) to do the same, but with no success.

Selections based on distance do work fine in both cases, but based on beta
value seem not to work properly.

here is the code I was trying to use:

atomselect macro bett { beta > 4}

mol representation VDW 0.700000 20.000000
mol color Name
mol material Opaque
mol selection {bett}
mol addrep top
set molid 0
set n [molinfo $molid get numreps]
for {set i 0} {$i < $n} {incr i} {
    mol selupdate $i $molid on
}

animate goto start

Can anyone help me with utilizing beta field to visualize changing number
of atoms during trajectory or give a clue hove to obtain this goal in some
other way?

PaweĊ‚