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

Dear Jeff, I am sorry for the delay in reply you. The error can be overcome by running phenix.den_refine (with parallelization) but alone. I mean: it is not possible to run multiple phenix.den_refine tasks, for example in two different console. This would probably occupy the .py subroutine whose error were reported. What do you think about this explanation? If I run phenix.den_refine with any parameters in den_refine.parameter file, it runs fine. Bye Fulvio Il giorno mar, 04/09/2012 alle 09.42 -0700, Jeff Headd ha scritto:

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 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 > > > _______________________________________________ > phenixbb mailing list > [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb > > > > _______________________________________________ > phenixbb mailing list > [email protected] > http://phenix-online.org/mailman/listinfo/phenixbb

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