[phenixbb] phenix.refine crashes

Nathaniel Echols nechols at lbl.gov
Tue May 8 07:40:02 PDT 2012

Ah, I see what is wrong - the Richardson lab updated the Ramachandran
distributions to use six different classes of amino acids, and I'm
still referencing the original four.  Will fix today.

FYI, the flip_peptides routine is still in an experimental state; I
need more examples of severely misfit peptides to test on.  It is
highly dependent on map quality right now, so if you're trying this on
a low-resolution structure, I wouldn't expect much, but in the future
we would like to use it to clean up regions of misbuilt secondary


On Tue, May 8, 2012 at 6:55 AM, Jianghai Zhu <jzhu at idi.harvard.edu> wrote:
> Hi,
> I am using phenix.refine dev-1051.  When I was trying flip_peptide, it crashes with the following error messages.
> Validate:
>                |--------START--------|  |--------FINAL--------|
>     residue    map_cc 2mFo-DFc mFo-DFc  map_cc 2mFo-DFc mFo-DFc
> Traceback (most recent call last):
>  File "/home/jzhu/phenix/phenix-dev-1051/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module>
>    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>  File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/command_line.py", line 146, in run
>    call_back_handler=call_back_handler)
>  File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/driver.py", line 1499, in run
>    ncs_manager             = self.ncs_manager)
>  File "/home/jzhu/phenix/phenix-dev-1051/phenix/phenix/refinement/strategies.py", line 928, in refinement_machine
>    params                      = params.flip_peptides)
>  File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/flip_peptides.py", line 445, in run
>    log=log)
>  File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/fit_rotamers.py", line 749, in validate_changes
>    sites_cart=sites_cart)
>  File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/refinement/flip_peptides.py", line 152, in __call__
>    return (self.rama_lookup.evaluate_sites(res_type,i_seqs,sites_cart)<0.002)
>  File "/home/jzhu/phenix/phenix-dev-1051/cctbx_project/mmtbx/rotamer/ramachandran_eval.py", line 76, in evaluate_sites
>    "isoleucine or valine"])
> AssertionError
> -- Jianghai
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