> Hi Fulvio,
>
>
> The crash in phenix.den_refine that you are seeing is because you do
> not have individual_sites active in your refinement parameters. If you
> change your den.params file to read:
>
>
> 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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