[phenixbb] error message on dev-1145 during den session
Jeff Headd
jjheadd at lbl.gov
Tue Sep 4 09:42:36 PDT 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 <
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
> >
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> >
> >
> >
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