Using DIALS at Diamond Light Source

DIALS is centrally installed on the Linux computer systems at Diamond. You can load the default version of DIALS by typing at the command line:

$ module load dials

The default version of DIALS (and xia2, etc.) is usually fixed at the start of a run, however a more recent nightly build of DIALS may be available:

$ module load dials/latest

Tutorials

For the following tutorials we suggest using the latest version of DIALS:

$ module load dials/latest

The thaumatin dataset used in the Processing in Detail (Thaumatin) is centrally available on the Diamond filesystem at /dls/mx-scratch/dials_tutorial/i04_thaumatin/.

Using DIALS with xia2

As an alternative to running DIALS directly, support for DIALS has been added within xia2. You can use xia2 just as before, simply replacing -2d, -3d, etc. with -dials:

$ xia2 -dials /dls/mx-scratch/dials_tutorial/i04_thaumatin/
Environment configuration...
XIA2_ROOT => /dls_sw/apps/dials/latest/dials-dev20151124/modules/xia2
XIA2CORE_ROOT => /dls_sw/apps/dials/latest/dials-dev20151124/modules/xia2/core
Python => /dls_sw/apps/dials/latest/dials-dev20151124/build/../base/bin/python2.7
CCTBX => /dls_sw/apps/dials/latest/dials-dev20151124/modules
CCP4 => /dls_sw/apps/ccp4/64/6.5/update19/ccp4-6.5
CLIBD => /dls_sw/apps/ccp4/64/6.5/update19/ccp4-6.5/lib/data
CCP4_SCR => /tmp/tmpPJJ4I7
Working directory: /dls/mx-scratch/rjgildea/tmp/insulin
Free space:        175586.36 GB
Host: cs03r-sc-serv-16
Build: v0.4.0.0-94-gf62dc5d
Contact: xia2.support@gmail.com
XIA2 0.4.0.0
DIALS 1.0-pre-210-gdd8f759
Command line: xia2 -dials /dls/mx-scratch/dials_tutorial/i04_thaumatin/
------------------- Autoindexing SWEEP1 --------------------
All possible indexing solutions:
tP  57.79  57.79 150.01  90.00  90.00  90.00
oC  81.72  81.74 150.02  90.00  90.00  90.00
oP  57.80  57.77 150.01  90.00  90.00  90.00
mC  81.73  81.75 150.03  90.00  89.99  90.00
mP  57.77  57.80 150.02  90.00  90.02  90.00
aP  57.81  57.78 150.03  90.01  89.99  89.99
Indexing solution:
tP  57.79  57.79 150.01  90.00  90.00  90.00
-------------------- Integrating SWEEP1 --------------------
Processed batches 1 to 540
Standard Deviation in pixel range: 0.370000 0.450000
Integration status per image (60/record):
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
"o" => good        "%" => ok        "!" => bad rmsd
"O" => overloaded  "#" => many bad  "." => weak
"@" => abandoned
Mosaic spread: 0.066 < 0.066 < 0.066
-------------------- Preparing DEFAULT ---------------------
Likely spacegroups:
P 41 21 2
P 43 21 2
Reindexing to first spacegroup setting: P 41 21 2 (h,k,l)
--------------------- Scaling DEFAULT ----------------------
Resolution limit for NATIVE/SWEEP1:  1.36
--------------------- Scaling DEFAULT ----------------------
Resolution limit for NATIVE/SWEEP1:  1.36
Overall twinning score: 2.02
Your data do not appear twinned
Project: AUTOMATIC
Crystal: DEFAULT
Sequence:
Wavelength name: NATIVE
Wavelength 0.97625
Sweeps:
SWEEP SWEEP1 [WAVELENGTH NATIVE]
TEMPLATE th_8_2_####.cbf
DIRECTORY /dls/mx-scratch/dials_tutorial/i04_thaumatin
IMAGES (USER) 1 to 540
MTZ file: /dls/mx-scratch/rjgildea/tmp/insulin/DEFAULT/NATIVE/SWEEP1/integrate/dials_integrated.mtz
For AUTOMATIC/DEFAULT/NATIVE
High resolution limit                          1.36    6.08    1.36
Low resolution limit                          50.00   50.00    1.40
Completeness                                  99.8    99.8    97.8
Multiplicity                                   5.3     4.9     3.1
I/sigma                                       12.1    31.7     2.1
Rmerge                                       0.060   0.025   0.364
Rmeas(I)                                     0.074   0.031   0.508
Rmeas(I+/-)                                  0.074   0.031   0.488
Rpim(I)                                      0.031   0.014   0.272
Rpim(I+/-)                                   0.042   0.017   0.321
CC half                                      0.999   0.999   0.826
Wilson B factor                              8.873
Anomalous completeness                        97.5   100.0    77.3
Anomalous multiplicity                         2.6     3.1     1.8
Anomalous correlation                        -0.001   0.299  -0.024
Anomalous slope                              0.960   0.000   0.000
Total observations                           292195  3740    12288
Total unique                                 55487   767     3923
Assuming spacegroup: P 41 21 2
Other likely alternatives are:
P 43 21 2
Unit cell:
57.784  57.784 150.002
90.000  90.000  90.000
mtz format:
Scaled reflections: /dls/mx-scratch/rjgildea/tmp/insulin/DataFiles/AUTOMATIC_DEFAULT_free.mtz
mtz_unmerged format:
Scaled reflections (NATIVE): /dls/mx-scratch/rjgildea/tmp/insulin/DataFiles/AUTOMATIC_DEFAULT_scaled_unmerged.mtz
sca format:
Scaled reflections (NATIVE): /dls/mx-scratch/rjgildea/tmp/insulin/DataFiles/AUTOMATIC_DEFAULT_scaled.sca
sca_unmerged format:
Scaled reflections (NATIVE): /dls/mx-scratch/rjgildea/tmp/insulin/DataFiles/AUTOMATIC_DEFAULT_scaled_unmerged.sca
Processing took 00h 13m 16s
XIA2 used...  aimless ccp4 dials pointless xia2
Here are the appropriate citations (BIBTeX in xia-citations.bib.)
(1994) Acta Crystallogr. D 50, 760--763
Evans, Philip (2006) Acta Crystallographica Section D 62, 72--82
Winter, G. (2010) Journal of Applied Crystallography 43
Status: normal termination

Feedback

If you encounter any problems using DIALS or xia2, or indeed have any other feedback (positive or negative - we love to hear from you either way), please contact dials-support@lists.sourceforge.net or xia2.support@gmail.com respectively.