Does every MODEL ENDMDL have a unique Connection list?
Can you show me your PDB file?
Jordan
On Oct 5, 2012, at 1:59 AM, Vishwas Vasisht <vishwas.vasi...@gmail.com> wrote:
> Hi Thomas,
>
> Thanks, it works for single frame. But when I use multiple frame (using
> MODEL and ENDMDL), the connections which i specified in the first frame
> is retained for rest of the frames. Am I doing some mistake in the way I wrote
> my PDB file?
>
> Regards
> Vishwas
>
> 2012/10/4 Thomas Holder <spel...@users.sourceforge.net>
> Hi Vishwas,
>
> you can use PDB format with CONECT records. You need to set connect_mode=1
> before loading the PDB file into PyMOL.
>
> http://pymolwiki.org/index.php/Connect_mode
>
> http://www.wwpdb.org/documentation/format33/sect10.html#CONECT
>
> Hope that helps.
>
> Cheers,
> Thomas
>
> Vishwas Vasisht wrote, On 10/04/12 16:52:
>
> Hi,
>
> I want to feed in a coordinates of atoms along with bond connection
> information. Since the bonding is based on some calculation I do, I need to
> include this information by hand.
> I tried to output the trajectory from my analysis in .mol format (following
> some example .mol file), but particles are overlapping on each other.
> Can somebody suggest me a better way to feed in coordinates and bonding
> information
> to pymol.
>
> Regards
> Vishwas
>
> --
> Thomas Holder
> MPI for Developmental Biology
> Spemannstr. 35
> D-72076 Tübingen
>
>
>
> --
> Whoever fights monsters should see to it that in the
> process he does not become a monster. And when
> you look into an abyss, the abyss also looks into you.
> -- Friedrich Nietzsche
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