VMD-L Mailing List

From: Melquiond (adrien.melquiond_at_ibpc.fr)
Date: Mon Jul 17 2006 - 12:59:39 CDT

Hi,

I rebuilt my structure with AMBER 8 and made a topology file. I join you the
two files, so you can have a look ... Nevertheless, these changes don't
affect "the odd looking" cartoon representation ! So, it remains me to
specify the lacking bonds with CONECT ...

Thank you for your help

Le Monday 17 July 2006 17:40, John Stone a écrit :
> Hi,
>   It looks to me like you're missing a few bonds, which is causing
> the cartoon representation to do odd things.  When loading files from
> the PDB format, VMD uses a distance-based bond search, and you've got
> a few that are far enough away that they're not making the cut.  This
> is the reason for the odd looking cartoon rep, it's as if you chopped
> up your protein into sections.  You could either specify bonds with
> CONECT records, make a PSF or other file with this information, or
> something along those lines. 

-- 
Adrien
-------------------------------------------------------
Adrien Melquiond, PhD student
Laboratoire de Biochimie Theorique, CNRS UPR 9080, IBPC
13, rue Pierre et Marie Curie, 75005 Paris - FRANCE -
Tel : +33 [0]1 58 41 51 63
Fax : +33 [0]1 58 41 50 26
Email : adrien.melquiond_at_ibpc.fr
www : http://www.ibpc.fr/~melquion
-------------------------------------------------------