Package: fast-dp
Fast DP: Fast Data Processsing with XDSIntroductionFast 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, its 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.Usagefast_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)
  -a ATOM, --atom=ATOM  Atom type (e.g. Se)
  -j NUMBER_OF_JOBS, --number-of-jobs=NUMBER_OF_JOBS
                        Number of jobs for integration
  -k NUMBER_OF_CORES, --number-of-cores=NUMBER_OF_CORES
                        Number of cores for integration
  -J MAXIMUM_NUMBER_OF_JOBS, --maximum-number-of-jobs=MAXIMUM_NUMBER_OF_JOBS
                        Maximum number of jobs for integration
  -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 limitConventional usage, e.g. on laptop, would be e.g:fast_dp ~/data/i04-BAG-training/th_8_2_0001.cbfgiving 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: 1277.6The 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 citeas a DOI for the
source code and / or:Winter, G. & McAuley, K. E.
“Automated data collection for macromolecular crystallography.”
Methods 55, 81-93 (2011).Please also cite XDS, CCTBX & CCP4:Kabsch, W.
“XDS.”
Acta Cryst. D66, 125-132 (2010)Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W., and Adams, P. D.
“The Computational Crystallography Toolbox: crystallographic algorithms
in a reusable software framework”
J. Appl. Cryst. (2002). 35, 126-136Winn, M. D. et al.
“Overview of the CCP4 suite and current developments”
Acta. Cryst. D67, 235-242 (2011)Dependenciesfast_dp depends on:XDSCCP4CCTBXIf 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.InstallationYou can install the latest release version of fast_dp from PyPI by loading
your CCTBX environment and then runninglibtbx.pip install fast_dpand update an existing installation to a newer version withlibtbx.pip install --upgrade fast_dpYou will then have to run eg.libtbx.configure libtbxto make sure all command line programs are set up correctly.Installation for developersIf you are a developer then you can runlibtbx.install fast_dpinstead. This will check out a development copy of fast_dp into the cctbx
modules directory and then install that to the system. To update your
development copy you will need to update the repository as usual and then
runlibtbx.python setup.py developin the source directory.Coding StandardsWith prejudice the style guide for fast_dp is consistent PEP8 as
implemented by blackhttps://black.readthedocs.io/en/stable/-
installation is close to trivial (pip3 install black) and runwith no
optionsi.e. in fast_dp directoryblack .will do what is needed to return the formatting to the defaults so
that the diffs show only the code diffs not any formatting
differences. There is no intention to be heavy handed about this, but
having a style guide helps developers who contribute as there is no doubt.AssumptionsThe 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.Supportfast_dp is provided with no guarantee of support however “best effort” support
will be provided on contactingscientificsoftware@diamond.ac.uk. Users may be
asked to provide example data in the event of a bug report.Acknowledgementsfast_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 its intrinsic parallelisation as well as CCP4 and CCTBX to operate, and
without these fast_dp could not exist.LicenseCopyright 2014 Diamond Light SourceLicensed 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 athttp://www.apache.org/licenses/LICENSE-2.0Unless 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.Release ProcessMake sure you have written up your changes in theHISTORY.rstfile.To prepare a new fast_dp release you need to installbump2version,
for example by runningpip install bump2versionor usinglibtbx.pipin an CCTBX environment, followed by alibtbx.configure. Releases can then be made by:# Assuming current version is 1.1.1
bumpversion major  # 1.1.1 -> 2.0.0
    # or
bumpversion minor  # 1.1.1 -> 1.2.0
    # or
bumpversion patch  # 1.1.1 -> 1.1.2

git push
git push origin v1.1.2
    # or
git push origin v1.2.0
    # or
git push origin v2.0.0The release tag, once pushed to Github, will be picked up by Travis
which will generate a new package and upload it directly to PyPI.History1.6.2 (2020-03-14)bugfix for Python 3 error1.6.1 (2020-02-25)add license file to release1.6.0 (2020-02-25)fast_dp is no longer supported with DIALS 1.12 and older versionsadd support for DIALS 2.1+add support for Python 3.81.5.0 (2019-10-23)add support for DIALS 2.0use correct number of cores for integration with forkxds1.4.0 (2019-06-10)Improved support for spacegroup names.
(#41)1.3.0 (2019-03-28)Report beam centre correctly in ispyb.xml for multi-panel
detectors.1.2.0 (2018-12-03)fast_dp and fast_rdp return with a non-zero exit code
when processing fails.1.1.2 (2018-11-22)Catch case where diffraction strong to edge of detector.1.1.1 (2018-11-21)Write out correct r_meas value in the fast_dp.json file.1.1.0 (2018-11-15)fast_dp.json format has changed. Scaling statistics are now
stored in a structured dictionary.
(#28)removed XDS.INP templates; now calculated on demand using dxtbx
models from DIALS, thus allowing support for all beamlines
currently understood by DIALS1.0.0 (2018-10-31)First release on PyPI.