refine {

strategy = *individual_sites rigid_body individual_adp \

group_adp tls occupancies group_anomalous *den

}

the refinement should work just fine.

I will add a check to make sure that this behavior is more clear.

Thanks,

Jeff

On Mon, Sep 3, 2012 at 1:10 AM, fulvio saccoccia <fulvio.saccoccia@uniroma1.it> wrote:

Dear Phenix users,

here you have an error occurred during a DEN refinement cycle on a
twinned structure. Please, help me in order to overcome the problem.

This is the command line I used to run phenix:
phenix.den_refine data.mtz model.pdb twin_law=h,-k,-l
output.prefix=DEN10 --overwrite main.ncs=true set_b_iso=50
convert_to_isotropic=true xray_data.high_resolution=3.6 nproc=4
secondary_structure_restraints=true optimize_xyz_weight=true
optimize_adp_weight=true reference_model.file=3ZVJ-coot1.pdb
use_geometry_restraints=true den.params fix_rotamers=true

den.params is attached

I was running phenix dev-1145 on a 64bit Debian machine.

This is the error message:

Running DEN torsion optimization on 4 processors...
Running torsion simulated annealing
...trying gamma 0.0, weight 100.0
...trying gamma 0.2, weight 100.0
...trying gamma 0.0, weight 300.0
...trying gamma 0.2, weight 300.0
Traceback (most recent call last):
File
"/usr/local/phenix-dev-1145/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/den_refine.py", line 21, in <module>
den_refine.run(command_name="phenix.den_refine", args=sys.argv[1:])
File
"/usr/local/phenix-dev-1145/phenix/phenix/refinement/den_refine.py",
line 113, in run
customized_master_params=master_phil)
File
"/usr/local/phenix-dev-1145/phenix/phenix/refinement/command_line.py",
line 146, in run
call_back_handler=call_back_handler)
File "/usr/local/phenix-dev-1145/phenix/phenix/refinement/driver.py",
line 1532, in run
ncs_manager = self.ncs_manager)
File
"/usr/local/phenix-dev-1145/phenix/phenix/refinement/strategies.py",
line 830, in refinement_machine
log=log)
File
"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line
88, in __init__
"serious error; please contact bugs@phenix-online.org.") % so)
RuntimeError: DEN weight optimization failed:
DEN cycle 1
rfree at start of SA cycle: 0.4642
k_rep = 1.00
tardy_tree summary:
number of vertices: 16570
number of edges: 16855
find cluster loops: 0 repeats
number of fixed vertex lists: 0
number of fixed vertices: 0
number of clusters: 7857
merge clusters with multiple connections: 1 pass
number of hinge edges: 7857
number of loop edges: 0
number of loop edge bendings: 0
number of fixed hinges: 0

CAUGHT EXCEPTION: (argument #0)
ARGUMENT LEADING TO EXCEPTION: (0.0, 100.0)
Traceback (most recent call last):
File "/usr/local/phenix-dev-1145/cctbx_project/libtbx/easy_mp.py",
line 155, in __call__
result = O.func(arg)
File
"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/den/refinement.py", line
227, in try_den_weight_torsion
call_back_after_step=False)
File
"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",
line 228, in run
reduced_geo_manager=reduced_geo_manager)
File
"/usr/local/phenix-dev-1145/cctbx_project/mmtbx/refinement/tardy.py",
line 86, in __init__
O.weights = target_weights.xyz_weights_result
AttributeError: 'NoneType' object has no attribute 'xyz_weights_result'

This is a serious error; please contact bugs@phenix-online.org.

Thanks in advance

Fulvio Saccoccia
PhD student
Dept. of Biochemical Sciences
Sapienza University of Rome
+390649910556

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