Hello pyMol Users, I have recently started working with pyMol. Here is my script, which one of the users (I am not sure whether it is right or not to write the name) has helped me to fix:
import os from pymol import cmd cmd.reinitialize() myDir = '/Users/User/myFolder' #print(myDir) for filename in os.listdir(myDir): print('HERE FILENAME is' , filename) if os.access(filename, os.R_OK): #check whether file exists and readable if ‘cif' in filename: #only cif format is needed cmd.load (filename) obj_name = os.path.splitext(filename)[0] filenameN = obj_name + '.mol' cmd.save(filenameN, obj_name) cmd.delete(obj_name) Here is the mistake log: File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/importing.py", line 819, in load _processCIF(cif,oname,state,quiet,discrete,_self) File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/importing.py", line 409, in _processCIF for i, rec in enumerate(cif): File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py", line 671, in next rec = CIFRec(self.datablocks_it.next()) File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py", line 226, in __init__ self.read_chem_comp_bond() File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py", line 575, in read_chem_comp_bond if self.read_chem_comp_bond_atom_ids(None, loop.keys, loop.rows): File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/chempy/cif.py", line 557, in read_chem_comp_bond_atom_ids name_dict[self.index_to_str(label_2,value)]] KeyError: ‘AtomName’ #atom name, e.g. ‘O’, ‘H2' Selector-Error: Invalid selection name «obj_name". (obj_name)<-- Traceback (most recent call last): File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/parsing.py", line 452, in run_file execfile(file,global_ns,local_ns) File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/parsing.py", line 447, in execfile b.execfile(filename, global_ns, local_ns) File "/Users/User/pyMolScript.py", line 13, in <module> cmd.save(filenameN, obj_name) File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/exporting.py", line 626, in save io.mol.toFile(_self.get_model(selection,state,ref,ref_state),filename) File "/usr/local/Cellar/pymol/1.7.2.1/libexec/lib/python2.7/site-packages/pymol/querying.py", line 1064, in get_model if _raising(r,_self): raise pymol.CmdException CmdException: Error: None Can you, please, tell how to fix this? And, if possible, what caused the mistake? Thank you, Best Regards, Alsa ------------------------------------------------------------------------------ _______________________________________________ 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