[phenixbb] trouble in phenix.refine

Huiying Li hli at zot.bio.uci.edu
Wed Nov 26 08:55:06 PST 2008

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:])
line 68, in run
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 Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
email: hli at uci.edu

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