Thanks Jason, your script works wonderfully.

On Thu, Dec 2, 2010 at 3:00 PM, Jason Vertrees <> wrote:
Hi Ramiro,

You have a couple options. áFirst 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

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).


-- Jason

On Thu, Dec 2, 2010 at 6:54 AM, Ramiro TÚllez Sanz <> 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:
> 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 TÚllez Sanz
> Dept. Physical Chemistry
> University of Almeria
> Spain
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Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(o) +1 (603) 374-7120