Cppxfel Installation

This details the installation instructions for cppxfel on Linux and Mac OS X. cppxfel relies on three components:

• Boost libraries (thread and system) - these allow C++ to access threading over multiple cores.
• DIALS distribution - provides the cctbx libraries for L-BFGS refinement and some crystallographic functions, and the indexing algorithms from DIALS itself.
• cppxfel distribution - primarily written in C++, but some Python scripts to automate DIALS indexing and prepare the results for input into cppxfel.

These installation instructions have been tested on CentOS 7.

DIALS distribution

Download the DIALS distribution for your flavour of OS (see [list of latest builds]) from [the DIALS website]. Ensure the distribution downloaded was compiled on 29th November 2015 or later for Boost thread support. Extract the dials-installer-dev to a new location. Navigate into this directory, e.g.:

cd dials-installer-dev

Start the install command to a new directory to which you have write access.

./install --prefix=/absolute/path/to/dials

cppxfel distribution

The cppxfel source code must be downloaded into the modules directory. Navigate to this directory, e.g.

cd /absolute/path/to/dials/dials-dev-508/modules

The repository can be cloned from the GitHub link for cppxfel.

git clone https://github.com/cppxfel/cppxfel.git

The build directory must be removed and recreated.

cd ..
rm -r build
mkdir build
cd build

The DIALS distribution must be configured to compile the xfel extension, and then the distribution must be compiled.

../base/bin/python ../modules/cctbx_project/libtbx/configure.py --enable_boost_threads=1 xfel
make

The same must be done for the cppxfel code.

../base/bin/python ../modules/cctbx_project/libtbx/configure.py --enable_boost_threads=1 cppxfel
make

Set the paths to the DIALS and cppxfel command line tools (bash):

Bash shell	Csh shell
. /absolute/path/to/dials/dials-dev-508/build/setpaths.sh	source /absolute/path/to/dials/dials-dev-508/build/setpaths.csh

This needs to be repeated every time a new shell is started. Alternatively, place this in your appropriate file (bash)

Bash shell	Csh shell
test -r /absolute/path/to/dials/dials-dev-508/build/setpaths.sh && \ . /absolute/path/to/dials/dials-dev-508/build/setpaths.sh	test -r /absolute/path/to/dials/dials-dev-508/build/setpaths.csh && \ source /absolute/path/to/dials/dials-dev-508/build/setpaths.csh
to ~/.bashrc	to ~/.cshrc

Alternate cppxfel-DIALS distribution for non-graphical High Performance Computing

Skip this section for typical use cases. On request from an HPC center, we give special instructions for building the Python library without importing graphics library code (instructions were tested on Centos 6.5). For a non-graphical installation do NOT start above with the DIALS distribution, instead start HERE:

wget --no-check-certificate https://raw.githubusercontent.com/cctbx/cctbx_project/master/libtbx/auto_build/bootstrap.py
python bootstrap.py hot update --builder=dials
python modules/cctbx_project/libtbx/auto_build/install_base_packages.py
cd modules
git clone https://github.com/cppxfel/cppxfel.git
cd ..
mkdir build
cd build
../base/bin/python ../modules/cctbx_project/libtbx/configure.py --enable_boost_threads=1 xfel
make
../base/bin/python ../modules/cctbx_project/libtbx/configure.py --enable_boost_threads=1 cppxfel
make

Set the paths to the DIALS and cppxfel command line tools:

Bash shell	Csh shell
. /absolute/path/to/build/setpaths.sh	source /absolute/path/to/build/setpaths.csh

This needs to be repeated every time a new shell is started. Alternatively, place this in your appropriate file:

Bash shell	Csh shell
test -r /absolute/path/to/build/setpaths.sh && \ . /absolute/path/to/build/setpaths.sh	test -r /absolute/path/to/build/setpaths.csh && \ source /absolute/path/to/build/setpaths.csh
to ~/.bashrc	to ~/.cshrc

CCP4 Symmetry libraries

The cppxfel distribution requires the CCP4 symmetry libraries. This needs to be pointed to by the SYMINFO environment variable. To set this:

Bash shell	Csh shell
export SYMINFO="/absolute/path/to/cctbx/modules/ccp4io/libccp4/data/syminfo.lib"	setenv SYMINFO /absolute/path/to/cctbx/modules/ccp4io/libccp4/data/syminfo.lib

This will prevent run-time errors from the CCP4 library functions not being able to find its symmetry information library. Consider adding these links to your ~/.bashrc or ~/.cshrc files to be executed on the generation of every new shell.

Check the installation

Confirm that cppxfel runs:

cppxfel.run

The output should look something like this:

Welcome to cppxfel version 1.0!
Please refer to & cite paper in Journal of Applied Crystallography (unpublished)

Command order for regular structure solution:
	cppxfel.run_dials shot*.pickle
	cppxfel.input_gen
	cppxfel.run -i integrate.txt
	cppxfel.run -i refine.txt
	cppxfel.run -i merge.txt

Other functions for assessing data quality:

Correlation between two MTZ files:

	cppxfel.run -cc firstFile.mtz secondFile.mtz [ambiguity] [lowRes] [highRes] [bins]

ambiguity: 0, 1, 2 or 3 - will compare different indexing solutions where the Bravais lattice symmetry is higher than that of the point group for certain space groups. Default 0
lowRes and highRes: set to resolution in Angstroms to bound the results, or set to 0 to take lowest/highest resolution data. Default 0, 0
bins: number of bins to report correlation statistics. Default 20.

Partiality CSV files:

	cppxfel.run -partiality reference.mtz ref-img-shot-number.mtz [highRes]

highRes: 0, 1, 2 or 3 - highest resolution reflection to report results on. Default 1.4
This outputs partiality_[m].csv where m is bin number, which can be imported into other graphing softwares such as R.

Merging statistics:

	cppxfel.run -rpim unmerged_file.mtz [lowRes] [highRes] [bins]
	cppxfel.run -rmeas unmerged_file.mtz [lowRes] [highRes] [bins]
	cppxfel.run -rmerge unmerged_file.mtz [lowRes] [highRes] [bins]

lowRes and highRes: set to resolution in Angstroms to bound the results, or set to 0 to take lowest/highest resolution data. Default 0, 0
bins: number of bins to report correlation statistics. Default 20.

If you see this, cppxfel has been installed.

Next steps

Try running the tutorial on a set of 1000 images from CPV, starting with indexing.