VMD-L Mailing List

From: Zhang, Tao (tao.zhang_at_pitt.edu)
Date: Wed Oct 21 2015 - 14:54:11 CDT

Hi, John

Thanks a lot. I do feel that would be useful to add a feature for coloring by bond order.

Best,

Tao

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Wednesday, October 21, 2015 3:50 PM
To: Zhang, Tao <tao.zhang_at_pitt.edu>
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: assign bond color based on bond type

Hi,
  If you're talking about mol2 bond order fields, at present VMD doesn't allow you to color by bond order, nor to select by bond order. VMD presently only uses the bond order information to affect the graphical representation of the bonds, but not other properties.
It would be relatively easy to add a feature for coloring by bond order if people feel that would be useful. VMD historically didn't do much with bond orders since many molecular file formats don't specify this information.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 21, 2015 at 03:53:26PM +0000, Zhang, Tao wrote:
> HI, I wish to draw different bonds with different colors based on the bond
> type. For example, bonds with bond type 1 are blue, bonds with bond type 2
> are yellow and bonds with bond type 3 are green. I want to emphasize that
> the color is based on bond type, NOT atom type! Is there any way to
> accomplish this? I am using mol2 file as input file and I can set bond
> type in mol2 format files.
>
>
>
> Thanks. 

--
NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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