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


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

3 comments:

biophysics said...

can I see the archives of xia2bb somewhere ? I have a few questions

fukamit3 said...

I want to know command line options in the log, like -lattice, -spacegroup, -beam, -3dii, etc.
Some options can be seen in the .xinfo file, but not all of them.

Graeme Winter said...

Command line will be copied to the log file now, as command line: ...

Regarding archives, I don't think that there are archives. I will check!