=============================================================================== The RNA-align program identifies the best alignment of two RNA (or DNA) structures with the highest TM-score. Please report suggestions and issues to yangzhanglab@umich.edu Reference to cite: Sha Gong, Chengxin Zhang, Yang Zhang. RNA-align: quick and accurate alignment of RNA 3D structures based on size-independent TM-scoreRNA. (2019) Bioinformatics. DISCLAIMER: Permission to use, copy, modify, and distribute this program for any purpose, with or without fee, is hereby granted, provided that the notices on the head, the reference information, and this copyright notice appear in all copies or substantial portions of the Software. It is provided "as is" without express or implied warranty. ========================= How to install RNA-align ========================= To compile the program in your Linux computer, simply enter make or g++ -static -O3 -ffast-math -lm -o RNAalign RNAalign.cpp The "-static" flag should be removed on Mac OS, which does not support building static executables. RNA-align natively supports PDB (.pdb) and PDBx/mmCIF (.cif) format input. If "zcat" or "bzcat" command is installed on your system, RNA-align can also read gzip compressed file (.pdb.gz or .cif.gz) or bzip2 compressed file (.pdb.bz2 or .cif.bz2). ===================== How to use RNA-align ===================== Briefly, to alignment two single-chain structures (Chain_1.pdb and Chain_2.pdb), enter the following: ./RNAalign Chain_1.pdb Chain_2.pdb You can run the program without arguments to obtain a brief instruction. Full document for all available options can be obained by: ./RNAalign -h 02/01/2019