[phenixbb] error message on dev-1145 during den session

[Jeff Headd]

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 at 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 at 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 at phenix-online.org.
>
> Thanks in advance
>
> Fulvio Saccoccia
> PhD student
> Dept. of Biochemical Sciences
> Sapienza University of Rome
> +390649910556
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120903/a07fd540/attachment.htm>