xalign

xalign is a multiple structral (cross) alignment tool written in Java. It can align two groups of protein structures against each other (one-to-one) and save the RMSD matrix as an Microsoft Excel file. Compiled binary is in the out/artifacts/xalign_jar folder.

You can use it in the command line with following commmand:

java -jar xalign.jar 1 group_1_pdbs.zip group_2_pdbs.zip path_to_results

Here 1 stands for the type of alignment algorithm. There are two distinct alignment algorithms that it can use:

1. FATCAT Rigid
2. FATCAT Flexible