Standarized file indentation
Shell script added which points to Scripts folder. Keeps all of the nitty-gritty stuff together in the scripts folder
Removed nonfunctional Bio3D scripts
Streamlined a2 analysis script. Merged scripts together from a2_create_dcd_no_H_or_H2O.tcl and a2_create_dcd_no_H_or_H2O_2.tcl. RMSD scan stuff moved to a5
Non-functional, so removed
New shell script points to ./Script folder
Incorporated rmsdscan, rmsfscan and radius of gyration scan from a2 into a5