[phenixbb] Death by Big-ass structure
Frank von Delft
frank.vondelft at sgc.ox.ac.uk
Fri May 25 10:36:05 PDT 2007
Wow, that was quick..... I'm impressed. Cool, I'll give it a swing.
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org] 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
>
>
>
>
> 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.
> > --
> >
> > _______________________________________________
> > phenixbb mailing list
> > phenixbb at phenix-online.org
> > http://www.phenix-online.org/mailman/listinfo/phenixbb
> >
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