It also has the same/analogous bug in space group P3 with Pointless
v1.2.10 - I wasn't sure if I was missing something obvious and went back
to using my default combination of REINDEX/SCALEIT for the tests and
reindexing.
Phil Jeffrey
Princeton
Robert Nolte wrote:
> An output file is created on hklout with or without the -copy flag.
> The problem is why is it picking the unity matrix (solution #2) for the
> reindexing operator rather than the first matrix (-h -k l) that it
> identifies under reindexing (which is clearly the correct answer).
>
> -----Original Message-----
> From: Jan Abendroth
> Sent: May 6, 2009 2:45 PM
> To: Robert Nolte
> Subject: Re: [ccp4bb] pointless question
>
> Hi Bob,
> including a -copy flag might not be totally pointless:
> pointless -copy hklin ...
>
> Jan
>
> 2009/5/6 Robert Nolte <[log in to unmask]
> <mailto:[log in to unmask]>>
>
> I'm hoping someone can help me with a pointless problem. I am
> trying to reindex
> data into an orientation that I used to solve the structure
> initially. While
> I can get pointless to give me the reindexing needed to make the
> new data match
> the old data for the project, when I ask it to write the data to
> HKLOUT it does
> not carry out the reindexing. I was under the impression from
> the documentation
> it would write out the reindexed solution. Am I doing something
> wrong or have
> I found a bug in my particular space group. I seem to recall
> getting this to work
> on a different project in the past. I have also tried a number
> of different
> versions of pointless, and all give me the same results. The
> output file is shown below.
> Thanks in advance for any help.
> Regards,
> Bob Nolte
>
>
> -> pointless hklin input.mtz hklref reference.mtz hklout
> reindex.mtz >& pointless.log
>
> contents of pointless.log
>
> ###############################################################
> ### CCP4 6.1: POINTLESS version 1.2.23 : 26/09/08##
> ###############################################################
> User: unknown Run date: 28/ 4/2009 Run time: 13:48:05
>
>
> Please reference: Collaborative Computational Project, Number
> 4. 1994.
> "The CCP4 Suite: Programs for Protein Crystallography". Acta
> Cryst. D50, 760-763.
> as well as any specific reference in the program write-up.
>
> OS type: linux
> Release Date: 26th September 2008
>
>
> ******************************************************
> * *
> * POINTLESS *
> * 1.2.23 *
> * *
> * Determine Laue group from unmerged intensities *
> * Phil Evans MRC LMB, Cambridge *
> * Uses cctbx routines by Ralf Grosse-Kunstleve et al.*
> * *
> ******************************************************
>
>
> ---------------------------------------------------------------
>
> Reading reference data set from file reference.mtz
> Maximum resolution in file reference.mtz: 1.810
> Columns for F, sigF (squared to I): F_881 SIGF_881
> Number of valid observations read: 18733
> Highest resolution: 1.81
> Unit cell: 72.66 72.66 65.98 90.00 90.00 120.00
> Space group: P 3 2 1
>
> Spacegroup information obtained from library file:
> Logical Name: SYMINFO Filename:
> /apps/ccp4/ccp4-6.1.0/lib/data/syminfo.lib
>
> Maximum resolution in file input.mtz: 1.870
> Columns for F, sigF (squared to I): F_880 SIGF_880
> Number of valid observations read: 17028
> Highest resolution: 1.87
> Unit cell: 72.58 72.58 66.20 90.00 90.00 120.00
> Space group: P 3 2 1
>
> Possible alternative indexing schemes
> Operators labelled "exact" are exact by symmetry
> For inexact options, deviations are from original cell
> (root mean square deviation between base vectors)
> Maximum accepted RMS deviation between test and reference
> cells (TOLERANCE) = 2.0
>
> [h,k,l] exact
> [-h,-k,l] exact
>
> >>>> Normalising reference dataset
>
> Log(<I>) fit for intensity normalisation: B (slope) -18.82
>
> >>>> Normalising test dataset
>
> Log(<I>) fit for intensity normalisation: B (slope) -18.21
>
> Alternative indexing relative to reference file reference.mtz
>
> $TEXT:Result:$$ $$
>
> Alternative reindexing CC R(E^2) Number
> Cell_deviation
> [-h,-k,l] 0.967 0.092 17012 0.14
> [h,k,l] 0.067 0.495 17011 0.14
> $$
>
> ===============================================================
>
> Copying merged MTZ file from input.mtz
> to reindex.mtz
>
> Reindexing operator [h,k,l]
>
> Real space transformation (x,y,z)
>
> Reindexed space group : P 3 2 1
> Crystal: HKL_base
> Cell: 72.58 72.58 66.2 90 90 120
> Crystal: unknown
> Cell: 72.58 72.58 66.2 90 90 120
>
> 17080 reflections copied to output file
>
> $TEXT:Reference: $$ Please reference $$
> P.R.Evans, 'Scaling and assessment of data quality' Acta Cryst.
> D62, 72-82 (2005).
> $$
>
>
>
>
> --
> --
> Jan Abendroth
> deCODE biostructures
> Seattle / Bainbridge Island, WA, USA
> work: JAbendroth_at_decode.com
> home: Jan.Abendroth_at_gmail.com <http://Jan.Abendroth_at_gmail.com>
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