Hi Kar Weng, This is possible with a Python script. Save the following to a file (e.g. "mae2pdb.py") and run it with PyMOL ("File > Run Script..." or use the "run" command). This will convert all .mae files from the current directory to .pdb files.
from pymol import cmd import glob for filename in glob.glob('*.mae'): cmd.load(filename) cmd.save(filename[:-4] + '.pdb') cmd.delete('*') Hope that helps. Cheers, Thomas On 20 Feb 2017, at 01:58, Kar Weng Ng <karweng.t...@gmail.com> wrote: > Dear Sir/Madam, > > I am final year School of Pharmacy student, currently working on a homology > modelling project. I am relatively new to using PyMOL. I would like to > convert .mae ligand structures that were produced by glide_dock into .pdb > files. I understand that I could use the: load ligand_1.mae, then go to File > > Save molecule command. However I have thousands of ligand files to convert. > May I know if there's a way or script that could do this in a faster way? > > Thank you for your time. > > Best Regards, > Ng Kar Weng > School of Pharmacy > Taylor's University Lakeside Campus, Malaysia -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net