Hi Frank, What is your spacegroup? Peter

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

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