VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Apr 09 2010 - 15:43:03 CDT

On Fri, Apr 9, 2010 at 4:34 PM, Ziemys, Arturas
<Arturas.Ziemys_at_uth.tmc.edu> wrote:
>
> If I load a plain PDB file and do as you have suggested, how to access the binding information after ?

if you want to use it for scripting, i suggest you use the topotools plugin API:

http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/
http://sites.google.com/site/akohlmey/software/topotools/

you can also access it via "mol getbonds", but that is not
a very convenient API. the "middleware" part of topotools
was written exactly to make it more convenient to use.

otherwise you can save it into a file format of your choice
that stores bonding information...

cheers,
   axel.

p.s.: btw, you can, of course, get exactly the DynamicBonds behavior, by
setting all atomic radii to the same value, sqrt(rc/2.0) if i am not mistaken.

>
>
> Arturas
>
>
>
>
> From: Axel Kohlmeyer [akohlmey_at_gmail.com]
> Sent: Friday, April 09, 2010 3:23 PM
> To: Ziemys, Arturas
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: DynamicBonding
>
> On Fri, Apr 9, 2010 at 3:10 PM, Ziemys, Arturas
> <Arturas.Ziemys_at_uth.tmc.edu> wrote:
>> Hi,
>>
>> Is there any way access "DynamicBonding' information ? For example, to save to PDB with CONNECT records, or MOL2. Can I access by script ?
>
> you can actually do better. the Dynamic Bonds representation has a fixed cutoff
> for all atom distances.
>
> if you do:
>
> mol bondsrecalc [molinfo top]
>
> VMD will recalculate your bonding information based on
> atom dependent (covalent) atomic radii (initially from an internal table,
> but you can reset them). that will sort out all kinds of issue for bonding
> with atoms of largely differing radius.
>
> cheers,
>    axel.
>
>
>
>
>> Arturas
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
> 

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