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:
- FATCAT Rigid
- FATCAT Flexible