pymol-users

[PyMOL] CONECT card and STATES / damien

[Clavel <dc...@ib...>]

Hello PyMOL users,

I am currently puzzled by the CONECT card and the display of multi-states.
After, many trials I cannot end up with a correct representation of my work.

I loaded 9 states to PyMOL made of 2 different PDB files. The second 
files of each states contains specific CONECT cards according to the 
index number of each atoms (inter residue connection).

When I run my script, Pymol is working nicely except for the CONECT 
cards...
Basically, PyMOL only put in memory the CONECT card of the second files 
of the first state and apply it to the rest of the states.
In addition, I tried pdb_ignore_connect and connect_mode... Despites 
their fancy names those commands were useless.

Does someone knows how to force PyMol to read stricly PDB files when 
loading multi-states?

Many thanks.

-- 
*Damien CLAVEL*
PhD student at Laboratoire Chimie Physique (UP Sud)
                 and Institut de Biologie Structurale (EPN Campus)
--------------------------------------------------------------------------
Laboratoire de Chimie Physique 
<http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de 
Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
     Bul. 350 Campus Orsay                 EPN Campus
     15, Av. Jean Perrin                         6, rue Jules Horowitz
     F-91405 ORSAY Cedex                 F-38000 GRENOBLE

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Re: [PyMOL] CONECT card and STATES / damien

[Osvaldo M. <alo...@gm...>]

Hi Damien,

I am not sure if I understood you problem correctly.  Have you tried the
following commands?

set connect_mode, 2 (or other number)
load your_pdb_file_name.pdb, discrete=1

Cheers,
Osvaldo.


On Fri, Nov 28, 2014 at 12:23 PM, Clavel <dc...@ib...> wrote:

>  Hello PyMOL users,
>
> I am currently puzzled by the CONECT card and the display of multi-states.
> After, many trials I cannot end up with a correct representation of my
> work.
>
> I loaded 9 states to PyMOL made of 2 different PDB files. The second files
> of each states contains specific CONECT cards according to the index number
> of each atoms (inter residue connection).
>
> When I run my script, Pymol is working nicely except for the CONECT
> cards...
> Basically, PyMOL only put in memory the CONECT card of the second files of
> the first state and apply it to the rest of the states.
> In addition, I tried pdb_ignore_connect and connect_mode... Despites their
> fancy names those commands were useless.
>
> Does someone knows how to force PyMol to read stricly PDB files when
> loading multi-states?
>
> Many thanks.
>
> --
> *Damien CLAVEL*
>  PhD student at Laboratoire Chimie Physique (UP Sud)
>                 and Institut de Biologie Structurale (EPN Campus)
> --------------------------------------------------------------------------
>     Laboratoire de Chimie Physique
> <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/>    Institut de
> Biologie Structurale <http://www.ibs.fr/spip.php?lang=en>
>     Bul. 350 Campus Orsay                 EPN Campus
>     15, Av. Jean Perrin                         6, rue Jules Horowitz
>     F-91405 ORSAY Cedex                 F-38000 GRENOBLE
>
>    [image: Image and video hosting by TinyPic]
> <http://tinypic.com?ref=28s7yvd>
>
>
> ------------------------------------------------------------------------------
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