OK you're right, this is a bug in reindexing merged MTZ files relative
to a reference file (unmerged files are OK)
I've fixed this in version 1.3.8 available from our ftp site ftp.mrc-lmb.cam.ac.uk/pub/pre/
pointless-1.3.8.tar.gz source
pointless-1.3.8.linux Linux executable
pointless-1.3.8.osxi86 OSX executable
My apologies for this - I should have spotted the problem a long time
ago
Phil
On 6 May 2009, at 23:17, Robert Nolte wrote:
> Phil,
> I tried the version with 6.11, as well as the latest prebuilt
> version I could find on your site, 1.3.2. Both of them have the
> same behavior.
> The mtz file has F's in it. I get the same error when I try the
> I's from Truncate, and the original scalepack2mtz I's. However, if
> instead of using hklin with a MTZ file, I use scain with the
> scalepack file, the program functions as I think should. Thanks for
> looking into the problem.
> Bob Nolte
>
> -----Original Message-----
>> From: Phil Evans <[log in to unmask]>
>> Sent: May 6, 2009 5:28 PM
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] pointless question
>>
>> I think Pointless 1.2.23 was a broken version which escaped to the
>> wild in CCP4 release 6.1.0. The more recent release 6.1.1 has a fixed
>> version, and some more recent versions are also available from our
>> ftp
>> site
>>
>> eg ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.3.2...
>>
>> sorry about this
>>
>> Phil
>>
>>
>> On 6 May 2009, at 19:21, Robert Nolte wrote:
>>
>>> 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 $$
>>> P.R.Evans, 'Scaling and assessment of data quality' Acta Cryst.
>>> D62, 72-82 (2005).
>>> $$
>
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