Dear Biojava team,

When I was using the Biojava tool to perform tertiary structure alignment of proteins recently, I found that there was a problem of missing parameters in the protein comparison tool, which is important for automation.

Insufficient parameter occurs when calling FatCat program.
Biojava 7.1.1/4.0.0 -alignPair function failure
I read the help manual. According to the documentation and the past command line examples, I entered the command line as follow and it should not be missing any parameter. However in the latest version and all versions after 6.0.0 can not use this parameter -alignPair, may I ask is it invalid?

One more question of invalid of autoFetch function invalid in earliest version comparison tool
Biojava 7.1.1(latest version) autoFetch parameter run success

But Biojava 4.0.0 autoFetch parameter run failure— time out

I think maybe because the FatCat update and then the network protocal maybe different and the autofetch function need update also. So may I ask why 4.0.0 can not be used but latest version can be used?

Looking forward to your guidance and suggestions on these matters. Many thanks for any advice you can give.