Example 1 readme file.

In this example we use the C3' coarse-grained version 
of the tRNA crystal structure 6TNA (file 6TNA-C3.pdb) 
as the coarse-grained template.
Other files that need to be in the folder are:
6TNA-FD.txt (the fragment definition file)
6TNA-primary.txt (the primary sequence of the molecule)
baseConvert.pkl (a library for converting between base geomtries, look in the "scripts" folder if it is missing)
ex1a.py (the script for building the working library of full atomic fragments)
ex1b.py (the script for assembling a full atomic molecule)
1N32-subA.pdb (a subset of full atomic ribosomal RNA as a reference molecule)

Try example 1 in two steps:

Step 1:
Run part a of the example:
"python ex1a.py"
This script will build a working library of full atomic fragments. 
The script will print warnings if not enough matches are found for any fragments.

Step 2:
Run part b of the example:
"python ex1b.py"
This script will build a full atomic structure using the working library of full atomic fragments.


Example results can be found in the data/Ex1results folder.