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 <[email protected]
<mailto:[email protected]>>
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>
