DateFileSizeComment
10.2015 brickworx_v3.141.tgz 44MB Updated version. Fixed output model nomenclature errors
11.2014 motifs.tgz 18MB Latest set of RNA motifs
11.2014 1y3s_4.00A_lofi.mtz 36KB A low-resolution, high phase-bias example dataset (RNA-only)

INSTALLATION

You can download and install Brickworx on your computer. Currently only Unix-like systems are supported. The program has been tested most extensively under several versions of Ubuntu Linux (10.04/12.04/14.04), Centos 6.6, and OSX 10.9. If you find bugs under any other operating system, please let us know the details so we could fix them!

OSX

First, you will need to install Apple's developer tools (Xcode) and NumPy, a core package for scientific computing with Python. On recent OSX installations it can be done with two simple shell commands

xcode-select --install
sudo easy_install numpy

next unpack the archive

tar xvzf brickworx_v2.817.tgz
cd brickworx

and run a command

./brickworx.sh

If run for the first time the script will compile the program. Otherwise it will simply start Brickworx. The installation may take up to one hour, but you can speed it up specifying the number of CPUs to use, for example:

./brickworx.sh --scons_j 4

LINUX

First, install following packages

  1. python >= 2.6 (NOT Python3)
  2. python-dev (header files and a static library for Python)
  3. g++ >=4.4
  4. numpy >= 1.5 (core package for scientific computing with Python)

For example on Debian or Ubuntu you can simply type:

sudo aptitude install g++ python python-dev python-numpy

on Centos use the following:

sudo yum install gcc-c++ python python-devel numpy

next run a command

./brickworx.sh

If run for the first time the script will compile the program. Otherwise it will simply start Brickworx. The installation may take up to one hour, but you can speed it up specifying the number of CPUs to use, for example:

./brickworx.sh --scons_j 4

If you face any problems with the installation contact me at gchojnowski

QUICK START

1. Get test data from PDB REDO. Each entry page has a link "Conservatively optimised structure" at the bottom.
Click MTZ to download a map. e.g. 1ehz (tRNA dataset at 1.93 A resolution).

From command line you can simply run

wget http://www.cmbi.ru.nl/pdb_redo/eh/1ehz/1ehz_besttls.mtz

or if wget is not available on your system (e.g. OSX)

curl -O http://www.cmbi.ru.nl/pdb_redo/eh/1ehz/1ehz_besttls.mtz

2. List MTZ column labels

./brickworx.sh --mtzin=1ehz_besttls.mtz

 ==> Reading input map
 ==> Available MAP labels:
         FC,PHIC
         FC_ALL,PHIC_ALL
         FWT,PHWT
         DELFWT,PHDELWT
         FC_ALL_LS,PHIC_ALL_LS

3. Run program with a command

./brickworx.sh --mtzin=1ehz_besttls.mtz --labin=FWT,PHWT --rna