Please click here to go to the tutorial for DIALS 2.2.
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
DIALS 2.2 is available by typing:
$ module load dials/2
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
We suggest using this latest version of DIALS when trying the tutorials.
General¶
Using DIALS with xia2¶
As an alternative to running DIALS directly, DIALS can be run within xia2,
using pipeline=dials:
$ xia2 pipeline=dials /dls/mx-scratch/dials_tutorial/i04_thaumatin/
Environment configuration...
Python => /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20191028/build/../base/bin/python2.7
CCTBX => /dls/science/groups/scisoft/DIALS/CD/latest/dials-dev20191028/modules
CCP4 => /dls_sw/apps/ccp4/7.0.075/ccp4-7.0
CLIBD => /dls_sw/apps/ccp4/7.0.075/ccp4-7.0/lib/data
CCP4_SCR => /tmp/tmp4Xxusn
Starting directory: /dls/tmp/thaumatin
Working directory: /dls/tmp/thaumatin
Free space: 4229.16 GB
Host: cs03r-sc-serv-16
Contact: [email protected]
XIA2 0.6.257-g73f70f18-remotes/origin/dials-2.0
DIALS 2.dev.1038-gf37b0db7a
CCP4 7.0.075
Command line: xia2 pipeline=dials /dls/mx-scratch/dials_tutorial/i04_thaumatin
-------------------- Spotfinding SWEEP1 --------------------
120152 spots found on 540 images (max 2197 / bin)
* * * ** * ** **
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1 image 540
------------------- Autoindexing SWEEP1 --------------------
All possible indexing solutions:
tP 57.78 57.78 150.00 90.00 90.00 90.00
oC 81.72 81.74 150.02 90.00 90.00 90.00
oP 57.76 57.79 149.99 90.00 90.00 90.00
mC 81.74 81.75 150.04 90.00 89.99 90.00
mP 57.77 57.80 150.01 90.00 89.98 90.00
aP 57.78 57.81 150.03 89.99 89.99 90.01
Indexing solution:
tP 57.78 57.78 150.00 90.00 90.00 90.00
-------------------- Integrating SWEEP1 --------------------
Processed batches 1 to 540
Standard Deviation in pixel range: 0.41 0.51
Integration status per image (60/record):
%ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
"o" => good "%" => ok "!" => bad rmsd
"O" => overloaded "#" => many bad "." => weak
"@" => abandoned
Mosaic spread: 0.043 < 0.043 < 0.043
-------------------- Preparing DEFAULT ---------------------
--------------------- Scaling DEFAULT ----------------------
Completed a round of scaling using dials.scale
Resolution for sweep NATIVE/SWEEP1: 1.17 (cc_half > 0.3, unmerged <I/sigI> > 0.25)
--------------------- Scaling DEFAULT ----------------------
Completed a round of scaling using dials.scale
---------------- Systematic absences check -----------------
Most likely space group: P 41 21 2
------------------- Unit cell refinement -------------------
Overall: 57.78 57.78 149.99 90.00 90.00 90.00
Overall twinning score: 2.09
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/tmp/thaumatin/DEFAULT/NATIVE/SWEEP1/integrate/13_integrated.refl
For AUTOMATIC/DEFAULT/NATIVE Overall Low High
High resolution limit 1.17 3.18 1.17
Low resolution limit 53.92 53.98 1.19
Completeness 82.2 100.0 7.8
Multiplicity 4.5 5.4 1.0
I/sigma 10.0 46.6 0.4
Rmerge(I) 0.070 0.032 0.356
Rmerge(I+/-) 0.062 0.029 0.000
Rmeas(I) 0.078 0.035 0.503
Rmeas(I+/-) 0.077 0.035 0.000
Rpim(I) 0.034 0.015 0.356
Rpim(I+/-) 0.043 0.020 0.000
CC half 0.998 0.998 0.700
Wilson B factor 9.005
Anomalous completeness 71.3 99.2 0.3
Anomalous multiplicity 2.6 3.1 1.0
Anomalous correlation -0.012 -0.060 0.000
Anomalous slope 0.705
Total observations 321472 25415 339
Total unique 70801 4729 328
Assuming spacegroup: P 41 21 2
Unit cell (with estimated std devs):
57.78346(8) 57.78346(8) 149.9943(3)
90.0 90.0 90.0
mtz format:
Scaled reflections: /dls/tmp/thaumatin/DataFiles/AUTOMATIC_DEFAULT_free.mtz
mtz_unmerged format:
Scaled reflections (NATIVE): /dls/tmp/thaumatin/DataFiles/AUTOMATIC_DEFAULT_scaled_unmerged.mtz
Processing took 00h 06m 20s
XIA2 used... ccp4, dials, xia2
Here are the appropriate citations (BIBTeX in xia2-citations.bib.)
Winn, M. D. et al. (2011) Acta Cryst. D67, 235-242.
Winter, G. (2010) J. Appl. Cryst. 43, 186-190.
Winter, G. et al. (2018) Acta Cryst. D74, 85-97.
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.
