pymol-users

[PyMOL] How to modify toGroup script to also save individual .pdb files?

[Ramiro T. S. <urc...@gm...>]

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

Re: [PyMOL] How to modify toGroup script to also save individual .pdb files?

[Jason V. <jas...@sc...>]

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 <urc...@gm...> 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) Jas...@sc...
(o) +1 (603) 374-7120

Re: [PyMOL] How to modify toGroup script to also save individual .pdb files?

[Ramiro T. S. <urc...@gm...>]

Thanks Jason, your script works wonderfully.

On Thu, Dec 2, 2010 at 3:00 PM, Jason Vertrees <
jas...@sc...> 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 <urc...@gm...>
> 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
> >
> >
> >
> ------------------------------------------------------------------------------
> > Increase Visibility of Your 3D Game App & Earn a Chance To Win $500!
> > 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
> > _______________________________________________
> > PyMOL-users mailing list (PyM...@li...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pym...@li...
> >
>
>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>