pymol-users

[PyMOL] Use of PyMOL for inspection and saving of docking results from Autodock

[Marko S <mar...@gm...>]

Hello,

I'm quite a novice user of PyMOL but I am already impressed at the speed and
beauty of the rendering. But I have some questions regarding it's use for
viewing results of Autodock.
So I normally proceed as follows, i open the PDB molecule say fetch BLABLA
and i get the pdb file...Then i have two options, one is to simply open the
.dlg file then i get only one ligand results which i scrool with the play
button to see all the results, but there is also an option (i use the
autodock plugin, and with that i get all of the results on the screen), but
the problem is how to save everything together in one pdb. file. I tried
with the "write complex.pdb" but it made a strange mess when i look with
other pdb viewers such as Viewerlite.
What can you suggest me to do?

Thank you for the answers!

Msev

Re: [PyMOL] Use of PyMOL for inspection and saving of docking results from Autodock

[Daniel S. <ds...@gw...>]

Hi Msev,

if you download the latest version you'll find what you're looking for. On the 
"Score/Rank"-page you can export docking scores and also docking poses in pdb 
format. If you save a list containing different ligands it might indeed look 
weired when you reload the file into pymol since pymol makes the bonds only 
based on the first model. But you can convert the poses.pdb to a mol2 file 
with babel and load that into pymol. That should look nice.

Cheers,
Daniel

On Monday 15 February 2010 08:05:35 pm Marko S wrote:
> Hello,
> 
> I'm quite a novice user of PyMOL but I am already impressed at the speed
>  and beauty of the rendering. But I have some questions regarding it's use
>  for viewing results of Autodock.
> So I normally proceed as follows, i open the PDB molecule say fetch BLABLA
> and i get the pdb file...Then i have two options, one is to simply open the
> .dlg file then i get only one ligand results which i scrool with the play
> button to see all the results, but there is also an option (i use the
> autodock plugin, and with that i get all of the results on the screen), but
> the problem is how to save everything together in one pdb. file. I tried
> with the "write complex.pdb" but it made a strange mess when i look with
> other pdb viewers such as Viewerlite.
> What can you suggest me to do?
> 
> Thank you for the answers!
> 
> Msev
> 

-- 
Dr. Daniel Seeliger
Computational Biomolecular Dynamics Group
Max-Planck-Institute for Biophysical Chemistry
Tel. +49 (0) 551-201-2310
http://wwwuser.gwdg.de/~dseelig

Re: [PyMOL] Use of PyMOL for inspection and saving of docking results from Autodock

[Marko S <mar...@gm...>]

I already have the new plugin, and unfortunately only the part to view poses
and  export the results works for me, but it has a great potential if the
bugs are fixed so great work DanieI.
I make something useful when i converted the poses.pdb to poses.mol2 so
thank you. If i may ask you one more off topic question maybe directly on
your mail concerning Autodock, about some false results (results which
aren't like we expect them to be), if you have some spare time to answer
that?

Thank you for the answer!

Mark

2010/2/15 Daniel Seeliger <ds...@gw...>

> Hi Msev,
>
> if you download the latest version you'll find what you're looking for. On
> the
> "Score/Rank"-page you can export docking scores and also docking poses in
> pdb
> format. If you save a list containing different ligands it might indeed
> look
> weired when you reload the file into pymol since pymol makes the bonds only
> based on the first model. But you can convert the poses.pdb to a mol2 file
> with babel and load that into pymol. That should look nice.
>
> Cheers,
> Daniel
>
> On Monday 15 February 2010 08:05:35 pm Marko S wrote:
> > Hello,
> >
> > I'm quite a novice user of PyMOL but I am already impressed at the speed
> >  and beauty of the rendering. But I have some questions regarding it's
> use
> >  for viewing results of Autodock.
> > So I normally proceed as follows, i open the PDB molecule say fetch
> BLABLA
> > and i get the pdb file...Then i have two options, one is to simply open
> the
> > .dlg file then i get only one ligand results which i scrool with the play
> > button to see all the results, but there is also an option (i use the
> > autodock plugin, and with that i get all of the results on the screen),
> but
> > the problem is how to save everything together in one pdb. file. I tried
> > with the "write complex.pdb" but it made a strange mess when i look with
> > other pdb viewers such as Viewerlite.
> > What can you suggest me to do?
> >
> > Thank you for the answers!
> >
> > Msev
> >
>
> --
> Dr. Daniel Seeliger
> Computational Biomolecular Dynamics Group
> Max-Planck-Institute for Biophysical Chemistry
> Tel. +49 (0) 551-201-2310
> http://wwwuser.gwdg.de/~dseelig
>
>
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