Hi Pavel, the error indeed disappeared but was unfortunately replace with another one; it seems to involve the function _rna_sugar_pucker_analysis, but I have only protein in my input. Jonathan ------------------------------------- Traceback (most recent call last): File "/usr/local/phenix-1.4-30/phenix/phenix/command_line/refine.py", line 19, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.4-30/phenix/phenix/refinement/command_line.py", line 68, in run log=log) File "/usr/local/phenix-1.4-30/phenix/phenix/refinement/command_line.py", line 227, in __init__ self.pdb_file_names) File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/utils.py", line 833, in process_pdb_files raw_records = raw_records) File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/utils.py", line 864, in _process_pdb_file log = self.log) File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2881, in __init__ log=log) File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 2029, in __init__ log=log) File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 1507, in __init__ prev_mm=prev_mm) File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 504, in __init__ prev_mm=prev_mm) File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", line 534, in _rna_sugar_pucker_analysis raise RuntimeError("Feature disabled because of known problems.") RuntimeError: Feature disabled because of known problems. Imre Törő wrote:

Dear Pavel,

One of my structure suffers exactly from the same PM twinning (b=sqrt(3)*a, gamma=119.8, C222(1)==>P6(3)22), but this involves then three twinned domains. Is it possible to specify both operators in phenix.refine, and if yes, how?

Thankx in advance,

Imre

Pavel Afonine írta:

...

Hi Jonathan,

this is a bug and it is fixed already. Please use one of the latest development versions of PHENIX:

https://www.phenix-online.org/download/phenix/nightly/

Pavel.

On 4/8/09 8:02 AM, jonathan elegheert wrote:

...

Dear Phenix developers,

I am rigid-body refining a PM-twinned structure (C2221 => P6x22) with the operators suggested from xtriage or SFcheck but I keep running into this same error (version 1.4.3 or latest cci aps bundles);

1/2*h-1/2*k,-3/2*h-1/2*k,-l 1/2*h+1/2*k,3/2*h-1/2*k,-l

Any suggestions as to how I can resolve this?

Many thanks in advance,

Jonathan Elegheert PhD student Ghent University Belgium

-------------------------------------------------------------------------

Traceback (most recent call last): File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/command_line/refine.py", line 16, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 89, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/driver.py", line 1121, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/strategies.py", line 190, in refinement_machine twin_law = sgtbx.rt_mx( params.twinning.twin_law ) RuntimeError: cctbx InternalError: /net/garter/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/rt_mx.cpp(230): Unsuitable value for rational rotation matrix.

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Yes, that solved it! Thanks ever so much, Jonathan Ralf W. Grosse-Kunstleve wrote:

...

raise RuntimeError("Feature disabled because of known problems.") RuntimeError: Feature disabled because of known problems.

I'm guessing this is because you have a .def parameter file from a previous version. You have to override the old setting, e.g. by adding

rna_sugar_pucker_analysis.use=False

to the command line, or edit the parameter file and change the value there.

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