Playing with XDS predictions (using Numpy)

This is a tutorial at ECACOMSIG computing school (Freudenstadt, August 2016)

In this tutorial we will implement calculation of spot positions in 3D space (x,y,φ) from XPARM.XDS.

Reference paper: W. Kabsch "Integration, scaling, space-group assignment and post-refinement" Acta Cryst. (2010). D66, 133-144

Test data: Thaumatin / Diamond Light Source I04 user training

If you want to run the script, you need to install

• Python2.7 with CCTBX and Numpy (1.8 or higher)
  • You can use phenix.python if you installed phenix-1.10.1
• XDS and generate_XDS.INP
• Adxv

How to run the script

1. Get sample data

mkdir th_8_2
cd th_8_2
wget https://zenodo.org/record/10271/files/th_8_2.tar.bz2
tar xvf th_8_2.tar.bz2

2. Prepare XDS.INP and run XDS (Alternatively, you can use XPARM.XDS in this repository)

mkdir xds
cd xds
generate_XDS.INP "../th_8_2_0???.cbf"
vi XDS.INP # Edit SPOT_RANGE= 1 27   JOB= XYCORR INIT COLSPOT IDXREF
xds_par

3. Run the script

phenix.python prediction.py ./XPARM.XDS 1.5 0.06928 1
# Usage:      prediction.py [XPARM.XDS] [d_min] [mosaicity] [frame numbers..]

4. Use Adxv to see predictions with image

adxv ../th_8_2_0001.cbf prediction_000001.adx

Note: to use ipython with phenix

Probably there is an easier way, but..

First, install easy_install and then ipython to phenix environment

wget https://bootstrap.pypa.io/ez_setup.py
phenix.python ez_setup.py
phenix.python -c "from setuptools.command.easy_install import main; main()" ipython

ipython can be started by:

phenix.python $PHENIX/modules/cctbx_project/libtbx/command_line/ipython_shell_start.py

Alternatively, libtbx.ipython command can be activated if you run $PHENIX/build/bin/libtbx.refresh.