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

Jeff Headd jjheadd at lbl.gov
Fri Sep 7 11:27:14 PDT 2012


Hi Fulvio,

There's no reason that I'm aware of why you can't use the same phenix
installation in multiple concurrent sessions, and I've just tried the
scenario you described and it worked fine, even with both jobs writing to
the same directory. Are you still getting the same error message, or is it
a different error?

Jeff

On Fri, Sep 7, 2012 at 12:35 AM, fulvio saccoccia <
fulvio.saccoccia at uniroma1.it> wrote:

> 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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> >         >         phenixbb at phenix-online.org
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> >         >
> >         >
> >         >
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