Sync of the official PDB database in couchdb. The database is searchable for properties like number of residues, residue percentages, molecular weight etc...
This documentation requires CentOS 7.0
We will need to:
- install CouchDB
- install PyMol to generate small images of the PDB
- install node to rsync PDB and create the couchDB
cd /usr/local/src
Download the program from sourceforge using lynx !!!
yum install lynx
It is full of redirect ... and with curl and get it is not obvious.
http://downloads.sourceforge.net/project/pymol/pymol/1.7/pymol-v1.7.4.0.tar.bz2?r=https%3A%2F%2Fwww.google.ch%2F&ts=1429190153&use_mirror=softlayer-ams Uncompress and untar
bzip2 -d pymol-v1.7.4.0.tar.bz2
tar -xvf pymol-v1.7.4.0.tar
yum install freeglut numpy freeglut-devel libpng libpng-devel PyOpenGL glew glew-devel libxml2-devel freetype-devel gcc gcc-c++ python-devel
python setup.py build install --home=/usr/local/pymol
ln -s /usr/local/pymol/bin/pymol /usr/local/bin/
Examples from command line:
- pymol -c 1XAA.pdb -d "as ribbon;spectrum count;set seq_view" -g 1XAA.png
- pymol -c 1XAA.pdb -d "orient; as cartoon;spectrum count;set seq_view" -d "png 1XAA, width=200, height=200"