VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 26 2012 - 15:51:14 CST

Hi,
  You should be using one of the "user" fields to store anything that
is time-varying. The current VMD PDB plugin does not try to store
the various PDB fields as time-varying data because the "beta" field in
VMD is not a time-varying field. That said, you can write a script
that will load the PDBs and copy their beta fields into the user field
for a given timestep if you like.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 26, 2012 at 10:41:15PM +0100, Pawel Siuda wrote:
> 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} {
> A A 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?
> PaweAA* 

-- 
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