Hi Huiying, 1) Looks like your PDB file is corrupted somehow... To know exactly what is wrong, I need to have a look at this file. Could you please send to me (please don't send it to the whole bulletin board)? 2) Just a remark: I'm wondering why you are running just "strategy=tls"?... It is much more efficient to do TLS refinement combined with coordinates refinement and total atomic B-factor refinement as well. By using "strategy=tls" you are refining only 20 TLS parameters per TLS group. Cheers, Pavel. On 11/26/2008 8:55 AM, Huiying Li wrote:
I was running phenix.refine in tls mode with the following command line:
phenix.refine mydata.mtz mymodel.pdb strategy=tls tls_group_selection.param mylibrary.cif
against a 2.1A data set, P21211 SG, a homodimer in AU, totally 10 tls groups. The following errors occured and program stopped. I do not know how to fix the problem.
Traceback (most recent call last): File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/command_line.py", line 68, in run log=log) .... ... .... File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/monomer_library/pdb_interpretation.py", line 970, in get_lib_link atom_dicts[angle.atom_3_comp_id].get(angle.atom_id_3, None)] IndexError: list index out of range
Your help is highly appreciated.
Huiying