Hey all! I am quite new to Rosetta and am using it for a project I am working on. My PI and I have found a paper in which we are wanting to use its code for minimizaiton and repacking but I really do not understand everything that is going on here. The code is as follows:
fix_bb_monomer_ddg.linuxgccrelease -ddg::weight_file soft_rep_design -ddg::iterations 50 - ddg::local_opt_only false -ddg::min_cst true -ddg::mean false -ddg::min true -ddg::sc_min_only false - ddg::ramp_repulsive true -ddg::minimization_scorefunction standard -ddg::minimization_patch score12
I can understand part of it.
1) I get that the 'fix_bb_monomer_ddg.linuxgccrelease' is invoking the packer (the syntax used in this code is weird cause I don't see any underscores in my Rosetta though)
2) I also get that the next couple parts are specifying the scoring function and the number of itterations
But now I get into the parts that I do not understand.
1) What is the 'ddg'? What does it mean and where does it come from? I have tried searching up Rosetta ddg on google but nothing really comes up for it.
2) Why are there so many double colons?
I am sure that the vast amjority of this is from my being so inexpoerienced but any help would be greatly appreciated. If anyone also has suggestions for extra Rosetta documention that would be amazing. I mainly use the tutorials provided but I can't seem to find a lot of this stuff on there. Thanks in advance!!