AE, you need to delete the loaded file before loading another. cmd.save will save ALL objects in the buffer by default as you have experienced yourself. Also your handling of the filename is slightly off, since pymol strips the extender upon loading, i.e. "test01.pdb" becomes "test01" object. You have two choices here, either you can retain all files in the buffer (not sure if this is your intention) or use Pymol as a file converter (you could use BABEL for that as well, might work better ?!). This is how I would write the code (untested however):
cmd.reinitialize() myDir = ‘/dirWithFiles' for filename in os.listdir(myDir): cmd.load (filename) obj_name = os.path.splitext(filename)[0] filenameN = obj_name + '.mol' cmd.save(filename, obj_name) cmd.delete(obj_name) # comment out this line of you want to keep all files in the buffer -----Original Message----- From: AE [mailto:alsalisb...@yahoo.com] Sent: Saturday, June 06, 2015 5:54 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] How to forbid merging of files? Good day, I have several thousands of files, which I upload using the loop: myDir = ‘/dirWithFiles' for filename in os.listdir(myDir): cmd.load (filename) filenameN = os.path.splitext(filename)[0] cmd.save(filenameN + '.mol') cmd.disable(filename) I am trying to save them one by one in a different (.mol) format. However, the files are saved together, i.e.: first file opened contains only molecule from the first file; second: first + second; third: first + second + third etc. But I want firstFile.readableFormat to be converted into firstFile.mol, secondFile.readableFormat - secondFile.mol etc, without any addition of other files. How can I do that? Thank you, Best Regards, Alsa Sorry I have sent it already, accidentally forgot to finish the question in subject( ------------------------------------------------------------------------------ _______________________________________________ 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 ------------------------------------------------------------------------------ _______________________________________________ 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