[PyMOL] RE : Pymol Scripts for Coarse grained for non-protein molecules

[ABEL S. 1. <Ste...@ce...>]

Hi Tsjerk,

Many thanks for your help, once again ;0 It works and it gives what i want. cool !!

Stephane
________________________________________
De : Tsjerk Wassenaar [ts...@gm...]
Date d'envoi : vendredi 1 mars 2013 13:56
À : ABEL Stephane 175950
Cc: pym...@li...
Objet : Re: [PyMOL] Pymol Scripts for Coarse grained for non-protein molecules

Hi Stephane,

You can convert a Gromacs run input file (.tpr) to a pdb file with
CONECT records using the Gromacs tool 'editconf' with the '-conect'
flag. The CONECT records will be set according to the bonds in the
topology. Pymol will read the CONECT records and set the bonds. If you
have a trajectory or a snapshot you want to visualize, you can load
the convert run input file first, and load the other structure(s) in
that object:

load tpr.pdb, cg
load traj.pdb, cg

Hope it helps,

Tsjerk


On Thu, Feb 28, 2013 at 1:18 PM, ABEL Stephane 175950
<Ste...@ce...> wrote:
> Hi all,
>
> I am looking for pymol scripts for showing coarse grained representation of non-protein molecules. I am currently using the sphere representation for each bead, but the bond between two beads are not shown, so it does not nice figures.
>
> Can you help me or give some advices
>
> Thanks you in advance
>
> Stephane
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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada