[ccp4bb] pointless question

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-05-06

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Subject: Re: pointless question
From: Robert Nolte rtnolte {- at -} EARTHLINK {- dot -} NET
Date: 2009-05-06

Subject: pointless question
From: Robert Nolte rtnolte {- at -} EARTHLINK {- dot -} NET
Date: 2009-05-06

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() fit for intensity normalisation: B (slope) -18.82

>>>> Normalising test dataset

Log() 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).
$$

CCP4bb navigation
CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Re: Refmac Question
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-05-06 Next message:
Subject: Re: pointless question
From: Robert Nolte rtnolte {- at -} EARTHLINK {- dot -} NET
Date: 2009-05-06