README.md

TBPyModeller

Template Based Modelling of Protein Structures in Python

#####Project coordinator:

Name	Handle
Xiaokai Qian	qxk2310

#####Team Members:

Name	Handle
Caiwei Wang	cwwmoment
Haipei Fan	happyfhp
Puneet Gaddam	pg7b2
Sean Lander	slander36
Brett Koonce	asparagui

Requirements:

#####Required:

• Python 3.3 32 bit
• Numpy 1.8 for Python 3.3 32 bit
• Biopython 1.63 for Python 3.3 32 bit
• Scwrl4

#####Optional:

• Jmol

To Run:

# Using ID and Sequence  
$ python TBModeller.py ID Sequence [ID Sequence...]  

# Using Fasta Files
$ python TBModeller.py file1.fasta [file2.fasta...]  

# Using DR Files (CASP)
$ python TBModeller.py file1.dr [file2.dr...]  

# Visualization with Jmol on Windows
C:\> set JMOL_HOME="{Jmol Directory Here}"
# Example: C:\> set JMOL_HOME="C:\Jmol"   
C:\> java -Xmx512m -jar %JMOL_HOME%\Jmol.jar targets\{targetid}.pdb

# Visualization with Jmol on Linux/Mac
$ export JMOL_HOME="{Jmol Directory Here}"
# Example: $ export JMOL_HOME="/home/user/Jmol"
$ java -Xmx512m -jar "$JMOL_HOME/Jmol.jar" targets/{targetid}.pdb