Introduction

XChemExplorer (XCE) is a data management and workflow tool for the parallel determination of protein-ligand structures. It was initially written to support crystallographic fragment screening at beamline I04-1 at the Diamond Light Source, but it is a generic program that can be used to facilitate any structure-based drug design project.

Current Version

v1.7.16 (08/10/2020)

Download

Please visit the XChem GitHub repository to download the latest version of XChemExplorer.

Mailing List

For questions, suggestions, hints, bug reports, please sign up to XCHEMBB@jiscmail.ac.uk

Operating System

LINUX
Mac OS X

Prerequisites:

CCP4 version 7.0 (or higher)
from v1.7.0 onwards: CCP4 version 7.1 (or higher)
PHENIX (optional, but recommended)

Presentations

Installation

Put the gzipped tar archive to wherever you want XCE to be installed. In case you have no root privileges, put it somewhere into your home directory, e.g.:

/home/tkrojer/software

Then change to the respective directory and unpack the archive, e.g.:

cd /home/tkrojer/software
gunzip XChemExplorer-1.2.tar.gz
tar –xvf XChemExplorer-1.2.tar

This will create a new directory, i.e. from now on your XChemExplorer directory. Change into this directory, e.g.:

cd XChemExplorer-1.2

The contents of the directory should look something like this when you type ‘ls –l’:

-rw-r--r--@  1 tobiaskrojer  staff     182 26 Jan 10:03 Dockerfile
-rw-r--r--@  1 tobiaskrojer  staff    2832 26 Jan 10:03 README.md
lrwxr-xr-x@  1 tobiaskrojer  staff      20 26 Jan 10:03 XChemExplorer -> XChemExplorer_dmd.sh
-rwxr-xr-x@  1 tobiaskrojer  staff  222991 26 Jan 10:03 XChemExplorer.py
-rwxr-xr-x@  1 tobiaskrojer  staff     316 26 Jan 10:03 XChemExplorer_dmd.sh
-rwxr-xr-x@  1 tobiaskrojer  staff     269 26 Jan 10:03 XChemExplorer_local.sh
-rw-r--r--@  1 tobiaskrojer  staff     465 26 Jan 10:03 compile_test.py
drwxr-xr-x@ 13 tobiaskrojer  staff     442 26 Jan 10:03 gui_scripts
drwxr-xr-x@ 14 tobiaskrojer  staff     476 26 Jan 10:03 helpers
drwxr-xr-x@ 10 tobiaskrojer  staff     340 26 Jan 10:03 icons
drwxr-xr-x@ 11 tobiaskrojer  staff     374 26 Jan 10:03 image
drwxr-xr-x@ 21 tobiaskrojer  staff     714 26 Jan 10:03 lib
-rwxr-xr-x@  1 tobiaskrojer  staff      43 26 Jan 10:03 run_tests
drwxr-xr-x@  5 tobiaskrojer  staff     170 26 Jan 10:03 setup-scripts
-rwxr-xr-x@  1 tobiaskrojer  staff     553 26 Jan 10:03 setupssh.sh
-rwxr-xr-x@  1 tobiaskrojer  staff     809 26 Jan 10:03 test_build.sh
drwxr-xr-x@  6 tobiaskrojer  staff     204 26 Jan 10:03 web

The only thing left to do is to edit the XChemExplorer_dmd.sh file. After you open XChemExplorer_dmd.sh with your editor of choice, the file will look like this:

#!/bin/bash

export XChemExplorer_DIR="/dls/science/groups/i04-1/software/XChemExplorer_new/XChemExplorer"
source $XChemExplorer_DIR/setup-scripts/xce.setup-sh
module unload ccp4
source /dls/science/groups/i04-1/software/pandda-update/ccp4/ccp4-7.0/bin/ccp4.setup-sh

ccp4-python $XChemExplorer_DIR/XChemExplorer.py

Change the first line (export XChemExplorer_Dir=…) to wherever you have the program installed (in the example, XChemExplorer is installed in /Users/tobiaskrojer/Downloads/XChemExplorer-1.2). And remove lines 3 and 4! After these edits, the file should look something like this:

#!/bin/bash

export XChemExplorer_DIR="/Users/tobiaskrojer/Downloads/XChemExplorer-1.1"
source $XChemExplorer_DIR/setup-scripts/xce.setup-sh

ccp4-python $XChemExplorer_DIR/XChemExplorer.py

That’s it!

Getting Started

You can now run XCE by typing

/Users/tobiaskrojer/Downloads/XChemExplorer-1.2/XChemExplorer

It may however be easier if you insert an alias into your .bashrc file:

alias XChemExplorer='/Users/tobiaskrojer/Downloads/XChemExplorer-1.1/XChemExplorer'

Manual - under development -

XChemExplorer v1.7.16

Reference

Krojer, T., Talon, R., Pearce, N., Collins, P., Douangamath, A., Brandao-Neto, J., Dias, A., Marsden, B., and von Delft, F. (2017). The XChemExplorer graphical workflow tool for routine or large-scale protein–ligand structure determination. Acta Cryst D 73, 267–278.

Contact

Tobias Krojer tobias.krojer@sgc.ox.ac.uk

Feature Requests

** under construction **

Resources

Example files for PDB group deposition

Example of XCE directory structure

xce_tutorial_data.zip