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

4 Sep 2012

      Hi Fulvio,

I'm sorry that you're still having trouble. I was able to run a test
refinement with your den.params input file when adding individual_sites as
a refinement strategy. Can you send me your most recent set of parameters
and perhaps any .log file that was generated directly to my email (not the
list) and I will take closer look.

Jeff

On Tue, Sep 4, 2012 at 4:14 AM, fulvio saccoccia <
[email protected]> wrote:
...
Dear all,
        I performed den refinement as suggested by Jeff Headd but it does
not
work. Just the: phenix.den_refine data.hkl model.pdb (without options at
all for den refinement) works. All attempt to use a den_refine.params
file (edited in such a way that parameters are different from default
ones) were unsuccesful.
Any advices is welcome
Thanks
Fulvio Saccoccia
PhD student
Dept. of Biochemical Sciences
Sapienza University of Rome
+390649910556
Il giorno lun, 03/09/2012 alle 11.06 -0700, Jeff Headd ha scritto:
...
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
 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 [email protected].") %
        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
        [email protected].
Thanks in advance
Fulvio Saccoccia
        PhD student
        Dept. of Biochemical Sciences
        Sapienza University of Rome
        +390649910556
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