Zhanglab forum

Hello,

When i read the the MMalign paper it's provide an option to optimize the interface match in addition to optimizing the TM-score.
However i’m not sure that i got the option in the help ?

Could you please tell me how can i use it?

Thank you

I have checked the source code and found that the program may automatically optimize the alignment of the interface residues because there is a part to identify the interface region.