edtools
Collection of tools for automated processing and clustering of batch 3-dimensional electron diffraction (3D ED) datasets.
The source for this project is available here.
Installation
Install using pip install edtools
. Installation should take less
than 20 seconds on a normal desktop.
Find the latest releases for the versions that have been tested on.
OS Requirement
Windows 10 or newer.
Software Requirements
Python 3.6+ including
numpy
,scipy
,matplotlib
, andpandas
libraries`sginfo
<https://github.com/rwgk/sginfo>`__ or`cctbx.python
<https://cctbx.github.io/installation.html#installation>`__ must be available on the system path foredtools.make_shelx
Access to WSL
XDS package must be installed properly under WSL
Package dependencies
Check pyproject.toml for the full dependency list and versions.
Documentation
See the documentation at https://edtools.readthedocs.io.
Pipeline tools
At any step, run edtools.xxx -h for help with possible arguments.
autoindex.py
Looks for files matching XDS.INP
in all subdirectories and runs them
using XDS
.
In: XDS.INP
Out: XDS data processing on all files
Usage:
edtools.autoindex
extract_xds_info.py
Looks files matching CORRECT.LP
in all subdirectories and extracts
unit cell/integration info. Summarizes the unit cells in the excel file
cells.xlsx
and cells.yaml
. XDS_ASCII.HKL files matching the
completeness / CC(1/2) criteria are listed in filelist.txt
.
Optionally, gathers the corresponding XDS_ASCII.HKL
files in the
local directory. The cells.yaml
file can be used as input for
further processing.
In: CORRECT.LP
Out: cells.yaml
cells.xlsx
filelist.txt
Usage:
edtools.extract_xds_info
find_cell.py
This program a cells.yaml file and shows histogram plots with the unit
cell parameters. This program mimicks
`CELLPARM
<http://xds.mpimf-heidelberg.mpg.de/html_doc/cellparm_program.html>`__
and calculates the weighted mean lattice parameters, where the weight is
typically the number of observed reflections (defaults to 1.0). For each
lattice parameter, the mean is calculated in a given range (default
range = median+-2). The range can be changed by dragging the cursor on
the histogram plots.
Alternatively, the unit cells can be clustered by giving the
--cluster
command, in which a dendrogram is shown. The cluster
cutoff can be selected by clicking in the dendrogram. The clusters will
be written to cells_cluster_#.yaml
.
In: cells.yaml
Out: mean cell parameters
cells_*.yaml (clustering only)
Usage:
edtools.find_cell cells.yaml --cluster
make_xscale.py
Prepares an input file XSCALE.INP
for XSCALE
and corresponding
XDSCONV.INP
for XDSCONV
. Takes a cells.yaml
file or a series
of XDS_ASCII.HKL
files as input, and uses those to generate the
XSCALE.INP
file.
In: cells.yaml / XDS_ASCII.HKL
Out: XSCALE.INP
Usage:
edtools.make_xscale cells.yaml -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmm
cluster.py
Parses the XSCALE.LP
file for the correlation coefficients between
reflection files to perform hierarchical cluster analysis (Giordano et
al., Acta Cryst. (2012). D68, 649–658). The cutoff threshold can be
selected by clicking in the dendrogram window. The program will write
new XSCALE.LP
files to subdirectories cluster_#
, and run
XSCALE
on them, and (if available), pointless.
In: XSCALE.LP
Out: cluster_n/
filelist.txt
*_XDS_ASCII.HKL
XSCALE processing
Pointless processing
shelx.hkl
shelx.ins (optional)
Usage:
edtools.cluster
Helper tools
make_shelx.py
Creates a shelx input file. Requires sginfo
to be available on the
system path to generate the SYMM/LATT cards.
In: cell, space group, composition
Out: shelx.ins
Usage:
edtools.make_shelx -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmm -m Si180 O360
run_pointless.py
Looks for XDS_ASCII.HKL files specified in the cells.yaml, or on the command line and runs Pointless on them.
In: cells.yaml / XDS_ASCII.HKL
Out: Pointless processing
update_xds.py
Looks files matching CORRECT.LP
in all subdirectories, and updates
the cell parameters / space group as specified.
In: XDS.INP
Out: XDS.INP
Usage:
edtools.update_xds -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmm
find_rotation_axis.py
Finds the rotation axis and prints out the inputs for several programs
(XDS, PETS, DIALS, Instamatic, and RED). Implements the algorithm from
Gorelik et al. (Introduction to ADT/ADT3D. In Uniting Electron
Crystallography and Powder Diffraction (2012), 337-347). The program
reads XDS.INP
to get information about the wavelength, pixelsize,
oscillation angle, and beam center, and SPOT.XDS
(generated by
COLSPOT) for the peak positions. If the XDS.INP
file is not
specified, the program will try to look for it in the current directory.
In: XDS.INP, SPOT.XDS
Out: Rotation axis
Usage:
edtools.find_rotation_axis [XDS.INP]
Demo of using edtools to process batch 3D electron diffraction datasets
See the demo at https://edtools.readthedocs.io/en/latest/examples/edtools_demo.html.
API Reference
- edtools
- edtools.autoindex
- edtools.cif_tools
- edtools.cluster
- edtools.extract_xds_info
- edtools.find_beam_center
- edtools.find_cell
- edtools.find_rotation_axis
- edtools.make_shelx
- edtools.make_xscale
- edtools.period_table
- edtools.reflection_tool
- edtools.run_pointless
- edtools.scattering_factor
- edtools.update_xds
- edtools.utils
- edtools.widgets
- edtools.wsl