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
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
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Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/
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