Re: [phenixbb] Death by Big-ass structure

25 May 2007


      Wow, that was quick.....  I'm impressed.  Cool, I'll give it a swing.
...
-----Original Message-----
From: [email protected] 
[mailto:[email protected]] On Behalf Of Peter Zwart
Sent: 25 May 2007 18:25
To: PHENIX user mailing list
Subject: Re: [phenixbb] Death by Big-ass structure
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
...
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
...
...
or should we go to the rhombohedral setting instead?
(Hmmmm, this rings a bell, wasn't there a posting about
2007/5/25, Paul Adams :
thought, 
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
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--
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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