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PDB Database

Sync of the official PDB database in couchdb. The database is searchable for properties like number of residues, residue percentages, molecular weight etc...

CouchDB replication of the PDB

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

Install PyMol

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

Install missing packages

yum install freeglut numpy freeglut-devel libpng libpng-devel PyOpenGL glew glew-devel libxml2-devel freetype-devel gcc gcc-c++ python-devel

Build the program

python setup.py build install --home=/usr/local/pymol
ln -s /usr/local/pymol/bin/pymol /usr/local/bin/

Convert a PDB to PNG

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"