From: Jason V. <jas...@sc...> - 2010-12-02 14:00:31
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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 |