VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Aug 13 2010 - 11:12:55 CDT

> The two problems I now have:
>
> 1. How do I get my bond distance to be based on the smoothing window
> coordinates rather than the "raw" per-frame coordinates?

you cannot. you would have to do the smoothing externally
and then feed the filtered coordinates back to VMD.
also there are better ways to denoise a trajectory than
what VMD currently offers. i have some prototype code
that i need for a different project and that might be
adapted for your purposes with reasonable effort.

please contact me personally, if you are interested in
starting a (small) project along those lines.

> 2. How do I delete incorrect bond selections, and accidental labels?

Open the Graphics->Labels dialog
there you can hide/delete/monitor all label items.

cheers,
   axel.

> Thanks,
>
> Ian 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.