[phenixbb] trouble in phenix.refine

Pavel Afonine pafonine at lbl.gov
Wed Nov 26 10:31:50 PST 2008

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.


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

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