Thanks Nat Got past that part but now a new error Traceback (most recent call last): File "/usr/local/phenix-dev-842/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-dev-842/phenix/phenix/refinement/command_line.py", line 96, in run call_back_handler=call_back_handler) File "/usr/local/phenix-dev-842/phenix/phenix/refinement/driver.py", line 1376, in run ncs_manager = self.ncs_manager) File "/usr/local/phenix-dev-842/phenix/phenix/refinement/strategies.py", line 489, in refinement_machine fmodels.fmodel_xray().update_f_part( AttributeError: 'manager' object has no attribute 'update_f_part' Immediately after bulk solvent modeling and scaling. F On Aug 14, 2011, at 5:29 PM, Nathaniel Echols wrote:

On Sun, Aug 14, 2011 at 4:26 PM, Francis E Reyes wrote:

...

Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 67, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 112, in __init__ hbond_params=self.params.hydrogen_bonding) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 494, in create_hbond_proxies log=log) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 286, in hydrogen_bond_proxies_from_selections log=log) File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/base_pairing.py", line 415, in create_hbond_proxies if distance_values[i][2] != '_': IndexError: tuple index out of range

When specifying a single base pair when using secondary_structure nucleic acids restraints

Could you please try the latest nightly build? This may have been fixed already.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Nat

The option "use_statistical_model_for_missing_atoms" is disabled until further notice - unfortunately, the current code does not actually warn you before it crashes. I'll fix that now.

How unfortunate! Statistical model for missing atoms was dropping my R/ Rfree about 10% (using 1.7.1-743). Is there a nightly that didn't drop use_statistical_model_for_missing_atoms but still has working secondary_structure nucleic acid restraints? I guess the other option is to generate the restraints myself .... F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Thanks Nat I've used this before and is useful when you have an already built structure (either your target structure or some simple A-form helices). For simple helices, it would be easier to specify a textual string and have phenix generate the proper restraints for phenix.refine (dihedrals, h-bonds, angles, etc). An excellent textual format for doing this is via stockholm. ftp://selab.janelia.org/pub/software/infernal/Userguide.pdf , specifically the SS_cons line.. (See the tRNA example in there). The current workflow, is to use coot to build an A-form helix and upload the file to PDBrestraints or use phenix.secondary_structure_restraints. Either case requires a sample pdb. F On Aug 15, 2011, at 9:51 AM, Nathaniel Echols wrote:

This may be a good intermediate solution:

http://rna.ucsc.edu/pdbrestraints/

I had meant to add an option to output the base pair restraints using the existing custom bond syntax, but haven't had time to do that yet.

-Nat

--------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder