Thanks Jason, your script works wonderfully.
On Thu, Dec 2, 2010 at 3:00 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Ramiro,
>
> You have a couple options. First you can select File > Save
> Molecule... from the upper control window and choose all the files, or
> you can run the 30-second old saveGroup command
> (http://www.pymolwiki.org/index.php/SaveGroup).
>
> It's easy to save a group to disk as one file ('save fileName.pdb,
> groupName') but splitting out the group's members take a little more
> effort (see the script).
>
> Cheers,
>
> -- Jason
>
> On Thu, Dec 2, 2010 at 6:54 AM, Ramiro Téllez Sanz <urcind...@gmail.com>
> wrote:
> > Thanks for reading this.
> >
> > I am doing docking studies with Vina, getting a single .pbqt file with
> > all the ligand poses. The magnificent toGroup script:
> > http://www.pymolwiki.org/index.php/ToGroup
> > allows me to easily create a single entry for each pose inside pymol,
> > making the saving of an individual .pdb file from each pose much more
> > convenient.
> >
> > Which command(s) must I include in the script so that it automatically
> > saves individual .pdb files from each extracted pose?
> >
> > On the other hand, I later create a single .sdf file containing all the
> > individually extracted pdb's from a terminal with the command:
> > babel -ipdb prefix*.pdb -osdf database.sdf
> >
> > Could this also be automated from the script, so that you run the script
> > toGroup on a loaded .pdbqt in PyMOL with multiple poses and end up with
> > a single .sdf?
> >
> > Thanks in advance,
> > Ramiro Téllez Sanz
> > Dept. Physical Chemistry
> > University of Almeria
> > Spain
> >
> >
> >
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>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
------------------------------------------------------------------------------
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Tap into the largest installed PC base & get more eyes on your game by
optimizing for Intel(R) Graphics Technology. Get started today with the
Intel(R) Software Partner Program. Five $500 cash prizes are up for grabs.
http://p.sf.net/sfu/intelisp-dev2dev
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