From: Antony Oliver
Date: 15 November 2011 17:06
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
----------
From: Graeme Winter
Dear Tony,
Sorry you found it hard to track me down - I should add a note on the
end of the log file as to how to report errors :o)
In order to work out what happened please could you send me (off list)
the xia2-debug.txt and xia2.error files?
Thanks & best wishes,
Graeme
----------
From: Graeme Winter
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
No comments:
Post a Comment