Hi all,

I'm trying to run PROMALS3D locally. To improve my alignments, I would like to add structural information. Unfortunately, to do so, I cannot just input the pdb files of the sequences I want to align (this option is only available on the webserver version). The developer of PROMALS has confirmed this. He told however that I could use constraint files instead.

Anyone an idea how I could obtain such constraint files from my pdb files?

On the webserver this is also possible: there it is explained that you can input "user-defined constraint alignments" (http://prodata.swmed.edu/promals3d/info/promals3d_help.html#inputconstraint). Is this just the output of any structure based alignment?

And how to input those constraint files in the command line of PROMALS3D?

Thanks a lot, Charlotte

Btw, in case you are wondering, I'm not just using the PROMALS3D webserver as I can only input 30 pdb files there and I have many more which could improve my alignment, it would be a pity to not be able to use them all.