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
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
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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participants (2)
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Jianghai Zhu -
Nathaniel Echols