VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 29 2006 - 14:27:46 CDT

Hi Ignacio,
  At present, there's a "trick". While we just barely had time to get
the dynamic bond recalculation code added for VMD 1.8.5 (a patch submitted
by Justin actually), there's presently not a way to set this mode in
the graphical interface. The way it is currently set is by an additional
representation parameter that specifies the distance cutoff to use, similar
to how the existing DynamicBonds rep is implemented:

Default drawing styles for mol 0, rep 0, No dynamic update:
   mol modstyle 0 0 Lines 1.0
   mol modstyle 0 0 CPK 1.0 0.3 8.0 6.0
   mol modstyle 0 0 Licorice 0.3 10.0 10.0
  
Dynamic update, cutoff distance of 1.6 (last parameter to each of these reps):
   mol modstyle 0 0 Lines 1.0 1.6
   mol modstyle 0 0 CPK 1.0 0.3 8.0 6.0 1.6
   mol modstyle 0 0 Licorice 0.3 10.0 10.0 1.6

Since there's not a GUI for this yet, I've written up a short Tcl
script that you can use to set all of the new dynamic-capable reps
to a cutoff of your choosing. To use the script, you run the command
(default cutoff of 1.6):
  setrepsdynamic 1.6

I've attached the script to this email. Let me know if you need help
using this feature.

The next rev of VMD should expose this in the graphical interface.
I may also change the behavior the text commands, but for now this is a
short-term method of using this feature more easily...

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 29, 2006 at 08:49:30AM +0100, Ignacio Fernández Galván wrote:
> Hi all,
>
> According to the 1.8.5 changelog, a new feature in this version is:
> "Dynamic reclalculation [sic] of bonds can now be set for several
> additional atom-oriented representations, for use with trajectory
> playback".
>
> When I read that I thought "great, now I can see bonds breaking and
> forming with lines or licorice representations, no need to select
> dynamicbonds everytime". However, I tried to do this and cannot get the
> bonds to change. Is there some trick? Did I misunderstand the
> changelog?
>
> Thanks.
>
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078