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

fulvio saccoccia fulvio.saccoccia at uniroma1.it
Fri Sep 7 00:35:51 PDT 2012


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
> <fulvio.saccoccia at 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 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
>         >
>         >
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