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.
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