VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 21 2020 - 13:42:10 CDT

You can set the radii for particular atoms using atom selection 'set'
commands, e.g. (silly example):
  set sel [atomselect top "name CA"]
  $sel set radius 5.0

If you don't have explicit bond information, you can then make
VMD re-guess your bond topology (for the top molecule) with:
  mol bondsrecalc top

You can recalculate VMD's interpretation of the the entire structure with:
  mol reanalyze top

If you search the mailing list and read the VMD scripting tutorials
you can do a lot with simple atom selection text commands like these.

Best,
  John

On Thu, Oct 08, 2020 at 09:18:30PM +0200, fulvio ciriaco wrote:
> dear vmd users,
> I have some badly distorted structures with bond lengths too long to be
> correctly recognized by vmd, I would like to modify the atomic radii
> table of vmd to obtain a better structure and visualization.
> Precisely there are inter residue dna bonds.
> How can this be done?
> yours
> Fulvio Ciriaco 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/