[phenixbb] Death by Big-ass structure

[Peter Zwart]

After you have installed phenix-1.3, try this


make a file named reindex.def that looks like this:


xmanip{
  input{
    unit_cell="80 80 130 90 90 120"
    space_group=R3:H
    xray_data
    {
      file_name=porin.cv
      labels=SIGMA
      label_appendix=None
      name = None
    }
    xray_data
    {
      file_name=porin.cv
      labels=TEST
      label_appendix=None
      name = None
    }
    model{
      file_name=porin.pdb
    }
  }
  parameters{
    action = *reindex operator manipulate_pdb xray_algebra
    reindex{
      standard_laws = *niggli reference_setting invert user_supplied
      user_supplied_law='h,k,l'
    }
  }
  output{
    logfile=xmanip.log
    hklout=xmanip.mtz
    xyzout=xmanip.pdb
  }
}

If you use mtz files, there is no need to give unit cell or space
group info, they will be picked up automatically.  Supply your pdb
file as well please.
Note that there are two xray_data scopes. You can add your free flag
here, and add additional scopes if you desire to place for instance
hendrickson lattman coefficients (they will be reindexed as well).

Labels should be unique identifiers for 'natural data groups', i.e.
for reading in columns FOBS,SIGFOBS,TEST, you only need to read in the
FOBS,SIGFOBS and TEST datasets.
unique labels might be S and T .

The action is in this case reindex, use the niggli operator to go to R3.


when you input file is done, run

phenix.python $PHENIX/mmtbx/mmtbx/xmanip.py reindex.def

This will produce new mtz and pdb files in the reindexed cell/space
group. Using this setting in phenix.refine will reduce memory
consumtion significantly and might speed up refinement.
Coot can handle refinement in this setting.
When you are ready for submission, just transform the lot back to what
you have by using the law 'reference_setting'

HTH

Peter




2007/5/25, Paul Adams <PDAdams at lbl.gov>:
> Hi Frank,
>
>    you should probably download the version 1.3 prerelease of PHENIX
> from the web page:
>
>    http://www.phenix-online.org/download/index.html
>
>    This may help.
>
>    Cheers,
>         Paul
>
>
> On May 25, 2007, at 8:12 AM, Frank von Delft wrote:
>
> > Hi, we get the memory error below for a structure of
> >       30603 atoms
> >       273217 reflections
> >       2.1A
> >       H3  193.868  193.868  352.223  90.00  90.00 120.00
> >       10x NCS
> >
> > Anything I said?  It's not THAT large a problem, I'd have thought,
> > or should
> > we go to the rhombohedral setting instead?
> >
> > (Hmmmm, this rings a bell, wasn't there a posting about this 3 days
> > ago?
> > Nothing in the archives, was it CCP4bb?)
> >
> > Cheers
> > phx
> >
> >
> >
> >
> > Traceback (most recent call last):
> >   File
> > "/usr/local/phenix/phenix-1.26b/phenix/phenix/command_line/
> > refine.py", line
> > 5, in ?
> >     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
> >   File
> > "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/
> > command_line.py",
> > line 75, in run
> >     refine_object.run(
> >   File "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/
> > driver.py",
> > line 1236, in run
> >     log                     = log)
> >   File
> > "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/
> > strategies.py",
> > line 273, in refinement_machine
> >     log                           = log)
> >   File
> > "/usr/local/phenix/phenix-1.26b/phenix/phenix/refinement/
> > weight_xray_chem.py
> > ", line 111, in __init__
> >     self.fmodel_copy = self.fmodel.deep_copy()
> >   File
> > "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/
> > twin_f_model.py", line
> > 1003, in deep_copy
> >     map_types          = self.map_types
> >   File
> > "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/
> > twin_f_model.py", line
> > 888, in __init__
> >     self.update_f_mask()
> >   File
> > "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/twinning/
> > twin_f_model.py", line
> > 1370, in update_f_mask
> >     self.f_mask_array = mask.structure_factors( self.miller_set )
> >   File "/usr/local/phenix/phenix-1.26b/mmtbx/mmtbx/masks.py", line
> > 103, in
> > structure_factors
> >     flex.grid(fft_manager.m_real()).set_focus(fft_manager.n_real()))
> > MemoryError
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> --
> Paul Adams
> Senior Staff Scientist, Physical Biosciences Division
> Head, Berkeley Center for Structural Biology
> Deputy Principal Investigator, Berkeley Structural Genomics Center
>
> Building 64, Room 248
> Tel: 510-486-4225, Fax: 510-486-5909
> http://cci.lbl.gov/
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
> --
>
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