dev_notes.md

MC-Search usage

• Step 1: Identify motives in desired structure Example for identifying all 7 nt loops:

cd output
../mcsearch -r ../motif/loop7.txt ../pdb/3cxc.pdb
gunzip 3cxc_model_1.pdb

• Step 2: Convert the output PDB into a structure database

../parse_pdb.py 

• MC-Annotate

../MC-Annotate -f 150 ./3cxc_model_1.pdb > 3cxc_annotations.txt
../mc-annotate_to_json.py 3cxc_annotations.txt

http://rna.bgsu.edu/rna3dhub/nrlist

http://www.major.iric.ca/wiki/index.php/MC-Search