[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
structure.
thanks,
Nat
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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