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 <fulvio.saccoccia@uniroma1.it> 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
> <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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>
>
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