Fast DP is a small Python program which uses XDS, CCP4 & CCTBX to deliver data processing results very quickly: quite how quickly will depend on the operating environment. In essence, the first image in the sweep is passed to the program, it's header read and then XDS used to index with a triclinic lattice using spots drawn from small wedges of data around the start, 45 degrees in and 90 degrees in (or as close as possible to this). Integration is then performed in parallel, either using multiple cores or multiple processors if the XDS forkintegrate script is appropriately configured. The data are then scaled with XDS, still in P1, before analysis with Pointless. Finally the analysis from Pointless and the global postrefinement results from the XDS CORRECT step are then used to select a pointgroup, after which the data are re-scaled with XDS in this pointgroup and merged with Aimless.
At Diamond Light Source, using an appropriately configured cluster with a parallel file store, this process typically takes up to two minutes for any number of images.
Usage:
fast_dp -h
Usage: fast_dp.py [options]
Options:
-h, --help show this help message and exit
-b BEAM, --beam=BEAM Beam centre: x, y (mm)
-d DISTANCE, --distance=DISTANCE
Detector distance: d (mm)
-a ATOM, --atom=ATOM Atom type (e.g. Se)
-j NUMBER_OF_JOBS, --number-of-jobs=NUMBER_OF_JOBS
Number of jobs for integration
-J MAXIMUM_NUMBER_OF_JOBS, --maximum-number-of-jobs=MAXIMUM_NUMBER_OF_JOBS
Maximum number of jobs for integration
-k NUMBER_OF_CORES, --number-of-cores=NUMBER_OF_CORES
Number of cores (theads) for integration
-l PLUGIN_LIBRARY, --lib=PLUGIN_LIBRARY
image reader plugin path, ending with .so
-e CLUSTER_NODES, -n CLUSTER_NODES, --execution-hosts=CLUSTER_NODES, --cluster-nodes=CLUSTER_NODES
-c CELL, --cell=CELL Cell constants for processing, needs spacegroup
-s SPACEGROUP, --spacegroup=SPACEGROUP
Spacegroup for scaling and merging
-1 FIRST_IMAGE, --first-image=FIRST_IMAGE
First image for processing
-N LAST_IMAGE, --last-image=LAST_IMAGE
Last image for processing
-r RESOLUTION_HIGH, --resolution-high=RESOLUTION_HIGH
High resolution limit
-R RESOLUTION_LOW, --resolution-low=RESOLUTION_LOW
Low resolution limit
Conventional usage, e.g. on laptop, would be e.g:
fast_dp ~/data/i04-BAG-training/th_8_2_0001.cbf
giving the following output on a 2011 Macbook Pro:
Fast_DP installed in: /Users/graeme/svn/fast_dp
Starting image: /Users/graeme/data/i04-BAG-training/th_8_2_0001.cbf
Number of jobs: 1
Number of cores: 0
Processing images: 1 -> 540
Phi range: 82.00 -> 163.00
Template: th_8_2_####.cbf
Wavelength: 0.97625
Working in: /private/tmp/fdp
All autoindexing results:
Lattice a b c alpha beta gamma
tP 57.80 57.80 150.00 90.00 90.00 90.00
oC 81.80 81.70 150.00 90.00 90.00 90.00
oP 57.80 57.80 150.00 90.00 90.00 90.00
mC 81.80 81.70 150.00 90.00 90.00 90.00
mP 57.80 57.80 150.00 90.00 90.00 90.00
aP 57.80 57.80 150.00 90.00 90.00 90.00
Mosaic spread: 0.04 < 0.06 < 0.07
Happy with sg# 89
57.80 57.80 150.00 90.00 90.00 90.00
--------------------------------------------------------------------------------
Low resolution 28.89 28.89 1.37
High resolution 1.34 5.99 1.34
Rmerge 0.062 0.024 0.420
I/sigma 13.40 44.70 1.60
Completeness 99.6 98.9 96.1
Multiplicity 5.3 5.0 2.8
Anom. Completeness 96.5 100.0 71.4
Anom. Multiplicity 2.6 3.1 1.2
Anom. Correlation 99.9 99.9 76.0
Nrefl 306284 3922 11217
Nunique 57886 786 4030
Mid-slope 1.007
dF/F 0.075
dI/sig(dI) 0.823
--------------------------------------------------------------------------------
Merging point group: P 4 2 2
Unit cell: 57.78 57.78 150.01 90.00 90.00 90.00
Processing took 00h 03m 59s (239 s) [306284 reflections]
RPS: 1277.6
The main result is the file fast_dp.mtz containing the scaled and merged intensities, a log file from Aimless for plotting the merging statistics and the information above in fast_dp.log.
See also fast_rdp to rerun last steps to change choices.
If you find fast_dp useful please cite 10.5281/zenodo.13039 as a DOI for the source code and / or:
Winter, G. & McAuley, K. E. "Automated data collection for macromolecular
crystallography." Methods 55, 81-93, doi:10.1016/j.ymeth.2011.06.010 (2011).
Please also cite XDS, CCTBX & CCP4:
Kabsch, W. "XDS." Acta Cryst. D66, 125-132 (2010)
R. W. Grosse-Kunstleve, N. K. Sauter, N. W. Moriarty and P. D. Adams
"The Computational Crystallography Toolbox: crystallographic algorithms
in a reusable software framework" J. Appl. Cryst. (2002). 35, 126-136
M. D. Winn et al. "Overview of the CCP4 suite and current developments"
Acta. Cryst. D67, 235-242 (2011)
fast_dp depends on:
- XDS
- CCP4
- CCTBX
If all of these are installed and configured no further work is needed. For parallel operation in integration a forkintegrate script is needed to send jobs to your queuing system.
Provided that the dependencies are all satisfied and the programs are on the PATH, all that is necessary is to unpack the fast_dp tarball and place the bin directory found therein into your PATH.
Optionally, you may manage paths or other initialization, by creating /etc/fast_dp/fast_dp.ini or $HOME/.fast_dp/fast_dp.ini, for example to set paths to find xds.
The XDS.INP files generated by fast_dp make the following assumptions:
- All scans are about a single axis, approximately parallel to the detector "fast" axis (multi-axis goniometers are fine provided the axis for the scan is fixed)
- The detector is not offset in two-theta i.e. the beam is approximately perpendicular to the detector face.
- Currently templates are included for Pilatus 2M & 6M, ADSC and Rayonix CCD detectors - modification to other detectors may be possible.
fast_dp is provided with no guarantee of support however "best effort" support will be provided on contacting scientificsoftware@diamond.ac.uk. Users may be asked to provide example data in the event of a bug report.
fast_dp was developed at Diamond Light Source with the specific purpose of providing feedback to users about the merging statistics of their data in the shortest possible time. Clearly, however, it is very much dependent on XDS and it's intrinsic parallelisation as well as CCP4 and CCTBX to operate, and without these fast_dp could not exist.
Copyright 2014 Diamond Light Source
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.