VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 21 2015 - 14:58:10 CDT

Tao,
  Can you send me an example .mol2 file that I can use for testing
to make sure that it works for your specific case? Please zip or gzip
a .mol2 file with the kind of structure you have in mind and I'll see if
I can get this added before I make the next round of VMD 1.9.3 test builds.
Once it's implemented and test builds are available I can send you an email
so you can try it out.

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Wed, Oct 21, 2015 at 07:54:11PM +0000, Zhang, Tao wrote:
> 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
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/