Dear Tony,
Many thanks for your additional help off list. The error is due to a
corner case relating to setting the spacegroup on the command line.
The fix is a one liner:
in $XIA2_ROOT/Modules/Scaler/CCP4ScalerR.py at line 451 please add
reindex_op = 'h,k,l'
to give something like:
Debug.write('Using input pointgroup: %s' % \
self._scalr_input_pointgroup)
pointgroup = self._scalr_input_pointgroup
reindex_op = 'h,k,l'
This will of course be mended in the next release.
Best wishes, and thankyou for the bug report.
Graeme
On 15 November 2011 17:06, Antony Oliver <[log in to unmask]> wrote:
> Dear CCP4 developers,
> Forgive the posting here, but I can't find the correct contact details for
> Graeme Winter…
> I have just downloaded the latest version of XIA2 (0.3.3.3 build 3479) and
> tried to integrate a dataset. The program fails with the following error…
>>>>
> Build: 3479
> XIA2 0.3.3.3
> Command line: xia2 -xinfo process.xinfo -spacegroup I212121
> ------------------- Autoindexing SWEEP1 --------------------
> All possible indexing solutions:
> oI 80.58 81.88 82.05 90.00 90.00 90.00
> oF 80.56 115.93 116.01 90.00 90.00 90.00
> mC 80.56 115.94 70.59 90.00 124.74 90.00
> Indexing solution:
> oI 80.58 81.88 82.05 90.00 90.00 90.00
> -------------------- Integrating SWEEP1 --------------------
> Processed batches 1 to 90
> Integration status per image (60/record):
> ooooooooooooooooooooooooooooooooooooooooooooooooooooooo%%%%%
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> "o" => good "%" => ok "!" => bad rmsd
> "O" => overloaded "#" => many bad "." => blank
> "@" => abandoned
> Mosaic spread: 0.530 < 0.660 < 0.770
> Need to rerun the integration...
> -------------------- Integrating SWEEP1 --------------------
> Processed batches 1 to 90
> Integration status per image (60/record):
> ooooooooooooooooooooooooooooooooooooooooooooooo%o%o%o%o%%%%%
> o%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> "o" => good "%" => ok "!" => bad rmsd
> "O" => overloaded "#" => many bad "." => blank
> "@" => abandoned
> Mosaic spread: 0.520 < 0.658 < 0.750
> ---------------------- Preparing DATA ----------------------
> Status: error "local variable 'reindex_op' referenced before assignment"
>>>>
> However, if I run exactly the same command set through an earlier version
> (0.3.3.1 build 3479) I have no problem…
>>>>
> Build: 3479
> XIA2 0.3.3.1
> Command line: xia2 -xinfo process.xinfo -spacegroup I212121
> ------------------- Autoindexing SWEEP1 --------------------
> All possible indexing solutions:
> oI 80.58 81.88 82.05 90.00 90.00 90.00
> oF 80.56 115.93 116.01 90.00 90.00 90.00
> mC 80.56 115.94 70.59 90.00 124.74 90.00
> Indexing solution:
> oI 80.58 81.88 82.05 90.00 90.00 90.00
> -------------------- Integrating SWEEP1 --------------------
> Processed batches 1 to 90
> Integration status per image (60/record):
> ooooooooooooooooooooooooooooooooooooooooooooooooooooooo%%%%%
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> "o" => good "%" => ok "!" => bad rmsd
> "O" => overloaded "#" => many bad "." => blank
> "@" => abandoned
> Mosaic spread: 0.530 < 0.660 < 0.770
> Need to rerun the integration...
> -------------------- Integrating SWEEP1 --------------------
> Processed batches 1 to 90
> Integration status per image (60/record):
> ooooooooooooooooooooooooooooooooooooooooooooooo%o%o%o%o%%%%%
> o%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> "o" => good "%" => ok "!" => bad rmsd
> "O" => overloaded "#" => many bad "." => blank
> "@" => abandoned
> Mosaic spread: 0.520 < 0.658 < 0.750
> ---------------------- Preparing TNKS ----------------------
> Likely spacegroups:
> I212121
> Reindexing to first spacegroup setting: I212121 (h,k,l)
>>>> NB: the program terminates normally.
> With regards,
> Tony.
>
> ---
> Dr Antony W Oliver
> Senior Research Fellow
> CR-UK DNA Repair Enzymes Group
> Genome Damage and Stability Centre
> Science Park Road
> University of Sussex
> Falmer, Brighton, BN1 9RQ
> email: [log in to unmask]
> tel (office): +44 (0)1273 678349
> tel (lab): +44 (0)1273 677512
>
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