ExaFEL / gui_demo

Install psana and cctbx

Construct conda environment on pslogin (conda version 4.6.14)

conda create -y -n gui_demo
conda activate gui_demo
conda install -y --channel lcls-rhel7 psana-conda
conda install -y future libtiff tqdm=4.23.4 wxpython=3
conda install -y -c conda-forge orderedset procrunner

Get CCTBX sources on pslogin

python bootstrap.py hot update --builder=xfel --cciuser=<username>

Build CCTBX on psana

python bootstrap.py build --builder=xfel --use-conda=${CONDA_PREFIX} --nproc=32

Starting GUI

source <CCTBX installation>/build/setpaths.sh
libtbx.python gui_demo/gui.py

Old instructions for Cori

conda

module load python
conda create -n gui_demo
source activate gui_demo

psana

conda install -y --channel lcls-rhel7 psana-conda
conda install -y -c conda-forge "mpich>=3" mpi4py h5py pytables libtiff=4.0.6
conda install -y scons
conda install -y wxpython libiconv Tornado

cctbx

python bootstrap.py hot update --builder=xfel --cciuser=<username> --sfuser=<username>
python bootstrap.py build --builder=xfel --with-python=`which python` --nproc=32
cd build; make

Coot

wget 'https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/binaries/release/coot-0.8.7-binary-Linux-x86_64-openSUSE-12.3-python-gtk2.tar.gz'
tar -xf coot-0.8.7-binary-Linux-x86_64-openSUSE-12.3-python-gtk2.tar.gz
wget 'https://ftp-osl.osuosl.org/pub/libpng/src/libpng15/libpng-1.5.29.tar.xz'
module load zlib
tar -xf libpng-1.5.29.tar.xz
cd libpng-1.5.29
./configure --prefix=<Coot directory>
make; make install

Running

module load python
source activate gui_demo
source <cctbx installation>/build/setpaths_all.sh
export COOT_PREFIX=<Coot directory>
export GUI_DEMO_PREFIX=<gui_demo directory>
python gui.py

Quick Start Guide

Guide to displaying beta-blip example. This requires downloading an example json, mtz, and pdb file.
Download gui_demo_example folder from https://stanford.box.com/s/khiepwwd7740u2u5s278rgj7infmwnq8
Unzip gui_demo_example.zip
This folder contains the directory structure:
.
+-- _beta-blip_refine
| +-- beta-blip_refine.json
| +-- beta-blip_refine_001.mtz
| +-- beta-blip_refine_001.pdb
Notice that the files must be named after the folder, i.e. filename starts with beta-blip_refine
Numbering convention for the pdb and mtz files start from 001 to 999. The electron density with the largest number will be displayed.
Json file contains the crystallography statistics.

conda activate gui_demo
source <cctbx installation>/build/setpaths_all.sh
export COOT_PREFIX=<Coot directory>
export GUI_DEMO_PREFIX=<gui_demo directory>
python gui.py -d <gui_demo_example directory>