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)
  -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 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 as 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, 126-136

Winn, M. D. et al. “Overview of the CCP4 suite and current developments” Acta. Cryst. D67, 235-242 (2011)

Installation for developers

If you are a developer then you can run

libtbx.install fast_dp

instead. 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 run

libtbx.python setup.py develop

in the source directory.

Coding Standards

With prejudice the style guide for fast_dp is consistent PEP8 as implemented by black https://black.readthedocs.io/en/stable/ - installation is close to trivial (pip3 install black) and run with no options i.e. in fast_dp directory

black .

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.