So I've been lucky enough to get the URL www.xia2.org, and sourceforge accounts for the different components (for hard-core individuals who want the very latest versions...) so I will start to migrate from the ccp4 servers shortly.
Right now I am trialling moving the xia2 downloads to:
ftp://ftpanon.diamond.ac.uk/xia2/
but for the forseeable, everything that is currently will remain.
As always, shout if you have any problems!
Thursday, 22 October 2009
Questions on program output
Hi Folks,
In an effort to finally tidy up the program output a little, I have made a start on slimming down the default (i.e. not -debug) program output. What I am looking at at the moment is something along the lines of that which follows below (a fixed-width font is probably a good idea here...)
So, here's the question: is there anything you think is currently missing from the program output? Anything that you always look at in a program log file (other than graphs: more on this below) which could be copied over? Anything which should be shouted loudly so you can find it easily?
In other news, Peter Briggs, of CCP4 fame, will now be looking at updating Baubles to take the plain text xia2 output and make it pretty, most likely as a web page, which should allow click-through access to things like the scala and truncate log files with the graphs therein rendered ... as graphs. If you have any interest in this please also shout on what you would like to see... at this end (i.e. at Diamond) we would like to get nice output visible through the web for remote-access users. It's also well over due for review anyway.
So, comments & questions please!
Many thanks,
Graeme
In an effort to finally tidy up the program output a little, I have made a start on slimming down the default (i.e. not -debug) program output. What I am looking at at the moment is something along the lines of that which follows below (a fixed-width font is probably a good idea here...)
So, here's the question: is there anything you think is currently missing from the program output? Anything that you always look at in a program log file (other than graphs: more on this below) which could be copied over? Anything which should be shouted loudly so you can find it easily?
In other news, Peter Briggs, of CCP4 fame, will now be looking at updating Baubles to take the plain text xia2 output and make it pretty, most likely as a web page, which should allow click-through access to things like the scala and truncate log files with the graphs therein rendered ... as graphs. If you have any interest in this please also shout on what you would like to see... at this end (i.e. at Diamond) we would like to get nice output visible through the web for remote-access users. It's also well over due for review anyway.
So, comments & questions please!
Many thanks,
Graeme
Environment configuration...
XIA2_ROOT => /home/gw56/CVS/xia2
XIA2CORE_ROOT => /home/gw56/CVS/xia2core
CCP4 => /scratch/xtal/ccp4/ccp4-6.1.1
CLIBD => /scratch/xtal/ccp4/ccp4-6.1.1/lib/data
BINSORT_SCR => /tmp/tmppNIYC2
Host: ws050
XIA2 0.3.0.6
------------------- Autoindexing SWEEP1 --------------------
All possible indexing solutions:
tP 51.80 51.80 158.18 90.00 90.00 90.00
oC 73.23 73.34 158.18 90.00 90.00 90.00
oP 51.79 51.84 158.18 90.00 90.00 90.00
mC 73.34 73.23 158.19 90.00 89.95 90.00
mP 51.80 158.18 51.86 90.00 89.91 90.00
aP 51.81 51.86 158.20 89.95 89.98 89.91
Indexing solution:
tP 51.80 51.80 158.18 90.00 90.00 90.00
Sweep epoch: 1096203695
-------------------- Integrating SWEEP1 --------------------
Processed batches 1 to 60
Integration status per image:
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
"o" => ok "%" => iffy rmsd "!" => bad rmsd
"O" => overloaded "#" => many bad "." => blank
Need to rerun the integration...
-------------------- Integrating SWEEP1 --------------------
Processed batches 1 to 60
Integration status per image:
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
"o" => ok "%" => iffy rmsd "!" => bad rmsd
"O" => overloaded "#" => many bad "." => blank
Stored integration parameters for crystal X12287
------------------- Autoindexing SWEEP2 --------------------
All possible indexing solutions:
tP 51.84 51.84 158.23 90.00 90.00 90.00
oC 73.22 73.51 158.27 90.00 90.00 90.00
oP 51.82 51.89 158.24 90.00 90.00 90.00
mC 73.51 73.22 158.28 90.00 89.93 90.00
mP 51.85 158.28 51.94 90.00 89.77 90.00
aP 51.86 51.95 158.28 89.93 89.97 89.77
Indexing solution:
tP 51.84 51.84 158.23 90.00 90.00 90.00
Using integration parameters for crystal X12287
Sweep epoch: 1096203943
-------------------- Integrating SWEEP2 --------------------
Processed batches 1 to 60
Integration status per image:
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
"o" => ok "%" => iffy rmsd "!" => bad rmsd
"O" => overloaded "#" => many bad "." => blank
--------------------- Preparing X12287 ---------------------
Likely spacegroups:
P 41 21 2
P 43 21 2
Reindexing to first spacegroup setting: P 41 21 2 (h,k,l)
---------------------- Scaling X12287 ----------------------
Resolution limit for INFL: 1.64
Resolution limit for LREM: 1.64
Optimised SD corrections (A, B) found to be:
Full: 0.03 12.0
Partial: 0.02 12.0
Computed average unit cell (will use in all files)
51.65 51.65 157.70 90.00 90.00 90.00
Overall twinning score: 2.13
Your data do not appear to be twinned
Inter-wavelength B and R-factor analysis:
INFL 0.0 0.00 (ok)
LREM 0.0 0.08 (ok)
Project: TB0541B
Crystal: X12287
Sequence:
Wavelength name: INFL
Wavelength 0.97966
Sweeps:
SWEEP SWEEP1 [WAVELENGTH INFL]
TEMPLATE 12287_1_E1_###.img
DIRECTORY /scratch/gw56/data/jcsg/als1/8.2.1/20040926/collection/TB0541B/12287
DETECTOR adsc
EXPOSURE TIME 5.100000
PHI WIDTH 1.00
IMAGES (USER) 1 to 60
MTZ file: /scratch/gw56/paper/12287/2d/X12287/INFL/SWEEP1/integrate/12287_1_E1__001.mtz
Wavelength name: LREM
Wavelength 1.00000
Sweeps:
SWEEP SWEEP2 [WAVELENGTH LREM]
TEMPLATE 12287_1_E2_###.img
DIRECTORY /scratch/gw56/data/jcsg/als1/8.2.1/20040926/collection/TB0541B/12287
DETECTOR adsc
EXPOSURE TIME 5.100000
PHI WIDTH 1.00
IMAGES (USER) 1 to 60
MTZ file: /scratch/gw56/paper/12287/2d/X12287/LREM/SWEEP2/integrate/12287_1_E2__001.mtz
For TB0541B/X12287/LREM
High resolution limit 1.64 7.33 1.64
Low resolution limit 52.57 52.57 1.68
Completeness 95.7 98.2 71.8
Multiplicity 4.2 3.3 2.6
I/sigma 13.9 27.2 2.2
Rmerge 0.053 0.032 0.354
Rmeas(I) 0.067 0.04 0.528
Rmeas(I+/-) 0.069 0.041 0.489
Rpim(I) 0.032 0.021 0.31
Rpim(I+/-) 0.043 0.026 0.336
Wilson B factor 18.959
Partial bias 0.005 -0.028 0.009
Anomalous completeness 94.3 98.9 67.7
Anomalous multiplicity 2.3 2.2 1.4
Anomalous correlation -0.234 -0.524 -0.021
Anomalous slope 0.869 0.0 0.0
Total observations 108108.0 1247.0 3576.0
Total unique 25995.0 375.0 1383.0
For TB0541B/X12287/INFL
High resolution limit 1.64 7.33 1.64
Low resolution limit 52.57 52.57 1.68
Completeness 97.4 98.0 79.8
Multiplicity 4.2 3.3 2.8
I/sigma 12.8 24.9 2.1
Rmerge 0.057 0.031 0.38
Rmeas(I) 0.097 0.068 0.582
Rmeas(I+/-) 0.073 0.041 0.513
Rpim(I) 0.045 0.035 0.328
Rpim(I+/-) 0.046 0.026 0.342
Wilson B factor 19.244
Partial bias -0.007 -0.04 0.011
Anomalous completeness 96.2 99.4 74.0
Anomalous multiplicity 2.3 2.2 1.5
Anomalous correlation 0.654 0.823 0.119
Anomalous slope 1.558 0.0 0.0
Total observations 111923.0 1248.0 4218.0
Total unique 26437.0 374.0 1526.0
Assuming spacegroup: P 41 21 2
Other likely alternatives are:
P 43 21 2
Unit cell:
51.649 51.649 157.697
90.000 90.000 90.000
mtz format:
Scaled reflections:
/scratch/gw56/paper/12287/2d/X12287/scale/TB0541B_X12287_free.mtz
sca format:
Scaled reflections (INFL):
/scratch/gw56/paper/12287/2d/X12287/scale/TB0541B_X12287_scaled_INFL.sca
Scaled reflections (LREM):
/scratch/gw56/paper/12287/2d/X12287/scale/TB0541B_X12287_scaled_LREM.sca
sca_unmerged format:
Scaled reflections (INFL):
/scratch/gw56/paper/12287/2d/X12287/scale/TB0541B_X12287_unmerged_INFL.sca
Scaled reflections (LREM):
/scratch/gw56/paper/12287/2d/X12287/scale/TB0541B_X12287_unmerged_LREM.sca
Processing took 00h 16m 48s
XIA2 used... ccp4 distl labelit mosflm pointless scala
Here are the appropriate citations (BIBTeX in xia-citations.bib.)
(1994) Acta Crystallogr. D 50, 760--763
Evans, P.R. (1997) Proceedings of CCP4 Study Weekend
Evans, Philip (2006) Acta Crystallographica Section D 62, 72--82
Leslie, AGW (1992) Joint CCP4 and ESFEACMB Newsletter on Protein
Crystallography 26
Leslie, Andrew G. W. (2006) Acta Crystallographica Section D 62, 48--57
Sauter, Nicholas K. and Grosse-Kunstleve, Ralf W. and Adams, Paul D.
(2004) Journal of Applied Crystallography 37, 399--409
Zhang, Z. and Sauter, N.K. and van den Bedem, H. and Snell, G. and
Deacon, A.M. (2006) J. Appl. Cryst 39, 112--119
Status: normal termination
Thursday, 15 October 2009
xia2 0.3.0.6 bug fix release
Hi Folks,
Time for some bug fixing & tidying. An unexpected side-effect of the changes allowing the setting of the cell constants etc. in the previous release was that the lattice tests no longer work for XDS. This is now fixed. Also the output has been tidied (fewer .txt files now) so that should help.
Here's the full text of the changes:
Changes since 0.3.0.5
* No lattice test mode added (you can guess the command-line option) for tricky data sets where this perhaps falls over.
* Fixed side effect of changes which allowed setting of unit cell etc. - lattices were no longer eliminated, failed complaining can't eliminate only solution.
* Tidied up the generation of output files and so on - now only have the main log file and the debug trace.
As always, shout if you have problems!
Time for some bug fixing & tidying. An unexpected side-effect of the changes allowing the setting of the cell constants etc. in the previous release was that the lattice tests no longer work for XDS. This is now fixed. Also the output has been tidied (fewer .txt files now) so that should help.
Here's the full text of the changes:
Changes since 0.3.0.5
* No lattice test mode added (you can guess the command-line option) for tricky data sets where this perhaps falls over.
* Fixed side effect of changes which allowed setting of unit cell etc. - lattices were no longer eliminated, failed complaining can't eliminate only solution.
* Tidied up the generation of output files and so on - now only have the main log file and the debug trace.
As always, shout if you have problems!
Wednesday, 30 September 2009
xia2-0.3.0.5: The FreeR release
New release, pretty minor except the FreeR calculations are much improved:
Changes since 0.3.0.4
* Now able to specify number or fraction of reflections assigned to the free set, rather than the default 5 percent.
* Added trap for sdcorrection not being refined in XDS correct if multiplicity rather low. Unusual case.
* Assigning a freer_file by definition sets this as an indexing reference and also copies the spacegroup assignment. This is what you would expect!
Changes since 0.3.0.3
* User now able to assign cell constants: use with great care, as there is little in the way of nonsense trapping. This may however be used to handle cases where the solution you want is monoclinic with a pseudo-orthorhombic lattice, where the default indexing would select a different setting. This will not currently work with a Mosflm indexer. Usage is:
-cell a,b,c,alpha,beta,gamma
and the correct symmetry should also be assigned. Can also assign USER_CELL a b c alpha beta gamma in the xinfo file.
Changes since 0.3.0.4
* Now able to specify number or fraction of reflections assigned to the free set, rather than the default 5 percent.
* Added trap for sdcorrection not being refined in XDS correct if multiplicity rather low. Unusual case.
* Assigning a freer_file by definition sets this as an indexing reference and also copies the spacegroup assignment. This is what you would expect!
Changes since 0.3.0.3
* User now able to assign cell constants: use with great care, as there is little in the way of nonsense trapping. This may however be used to handle cases where the solution you want is monoclinic with a pseudo-orthorhombic lattice, where the default indexing would select a different setting. This will not currently work with a Mosflm indexer. Usage is:
-cell a,b,c,alpha,beta,gamma
and the correct symmetry should also be assigned. Can also assign USER_CELL a b c alpha beta gamma in the xinfo file.
Tuesday, 15 September 2009
xia2-0.3.0.4 (quiet) release
Small change which I would like kinda tested before this becomes a mainstream feature: ability to assign unit cell constants and symmetry to use on the command-line and (untested) xinfo file.
More information at:
http://www.ccp4.ac.uk/xia/xia2-0.3.0.4.html
N.B. this is not linked as the default xia2 page, will be no xia2bb announcement.
More information at:
http://www.ccp4.ac.uk/xia/xia2-0.3.0.4.html
N.B. this is not linked as the default xia2 page, will be no xia2bb announcement.
Tuesday, 1 September 2009
xia2 0.3.0.3
Hi Folks,
A release update, 0.3.0.3 which includes a number of changes and very important bug fixes. Here are the main changes:
Changes since 0.3.0.0
* Now automatically determine the number of available processor cores.
* Implemented check for centring of crystallographic basis from autoindexing.
* Started to use CCTBX - this will be bundled with the release from now on...
* Now runs "smart scaling" i.e. will customise the scaling model used to the data. This can seriously improve the xia2 run time in cases where some of the default scaling models do not converge.
* Now also includes running of CHEF for radiation damage, which will slice and dice your data into dose groups, then run a correctly time sequenced radiation damage analysis. N.B. for data measured in "dose mode" the doses will be scaled to < 1,000,000 to ensure that the output is tidy.
* Corner case of running XDS pipelines from data from a Rigaku setup. The low resolution was previously calculated to be 0.0! D'oh!
* Added access to reference reflection file functionality to the command line - -reference_reflection_file foo.mtz.
* Fixed the use of the -image command-line option. Now works.
* Removed all of the binaries from the distribution, so now you need to be using CCP4 6.1.0 or later!
* Will correctly handle reindexing with the 3d pipeline (XDS/XSCALE) with trigonal spacegroups and multiple sweeps. Many thanks to Wolfgang Kabsch for a lot of help with this.
As things stand I don't include CCTBX - so you will need to have this installed, information at http://cci.lbl.gov.
A release update, 0.3.0.3 which includes a number of changes and very important bug fixes. Here are the main changes:
Changes since 0.3.0.0
* Now automatically determine the number of available processor cores.
* Implemented check for centring of crystallographic basis from autoindexing.
* Started to use CCTBX - this will be bundled with the release from now on...
* Now runs "smart scaling" i.e. will customise the scaling model used to the data. This can seriously improve the xia2 run time in cases where some of the default scaling models do not converge.
* Now also includes running of CHEF for radiation damage, which will slice and dice your data into dose groups, then run a correctly time sequenced radiation damage analysis. N.B. for data measured in "dose mode" the doses will be scaled to < 1,000,000 to ensure that the output is tidy.
* Corner case of running XDS pipelines from data from a Rigaku setup. The low resolution was previously calculated to be 0.0! D'oh!
* Added access to reference reflection file functionality to the command line - -reference_reflection_file foo.mtz.
* Fixed the use of the -image command-line option. Now works.
* Removed all of the binaries from the distribution, so now you need to be using CCP4 6.1.0 or later!
* Will correctly handle reindexing with the 3d pipeline (XDS/XSCALE) with trigonal spacegroups and multiple sweeps. Many thanks to Wolfgang Kabsch for a lot of help with this.
As things stand I don't include CCTBX - so you will need to have this installed, information at http://cci.lbl.gov.
Monday, 24 August 2009
Parallel mosflm & rotation axis
If you have a rotation axis which is not perpendicular to the beam (or very close to such) you may have noticed that the parallel integration sometimes falls over: this is because the postrefinement radius of convergence is ~ 1 degree, but the orientation may differ by more than this.
Next version I'll add support for the mosflm AUTOMATCH keyword which helps here, but only for mosflm version 7.0.5 as it was broken beforehand.
Next version I'll add support for the mosflm AUTOMATCH keyword which helps here, but only for mosflm version 7.0.5 as it was broken beforehand.
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