VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Dec 01 2016 - 15:09:27 CST

Hi,
  The VMD atom selection get/set syntax doesn't (yet) support writing all of
the timesteps at once. You must presently write a short loop that
does a "$sel frame" before doing the "$sel set ..." for each timestep.
You're on the right track, you just need to use a loop to get it done.
You could write a short Tcl proc to do the loop so that if you have
many of these to do that you won't have to cut-paste the loop logic
repeatedly.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Dec 01, 2016 at 02:05:28PM -0600, Brian Radak wrote:
> Apologies if this is a repeat.
>
> I am trying to make use of the "user" field in having a dynamic
> representation that changes at each time step. This is just a simple
> boolean that turns off or on a small set of atoms as part of a larger
> selection.
>
> How does one assign a time series to the user field? For each atom I
> have a Tcl list with size equal to the number of DCD frames, but the
> following does not seem to work:
>
> % set myProperty <list of size equal to numframes>
> % set sel [atomselect <selection for a single atom>]
> % $sel set user $myProperty
>
> Is "user" not a time dependent property by default? The help message for
> "atomselection set" does not seem to indicate any further keywords to
> flag that.
>
> Brian
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/