Help deciphering an input

[Anonymous]

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!!

[Anonymous]

The primary Rosetta documentation is here: https://www.rosettacommons.org/docs/latest/Home

Your starting point suggests you may benefit from the Meiler Lab recorded tutorials: http://www.meilerlab.org/index.php/rosetta-tutorials

> 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)

You are on command line.  fix_bb_monomer_ddg.linuxgccrelease is the command.  The remainder of the line is command line flags and arguments to those flags.  fix_bb_monomer_ddg.linuxgccrelease specifically is one compiled rosetta binary – the portion before the . names the binary (there are a few hundred) and the portion after describes how it was compiled.  I guess this command “invokes the packer” in a technical sense, but if all you want to do is repack you should use regular fixbb, as it is simpler and meant for the purpose.  

> 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. 

DDG means delta delta G – the change of free energy of folding upon mutation.  mutation is one delta, folding is one delta, g is gibbs free energy.  DDG of mutation tools tell how how a protein’s energy will change when you mutate the sequence but leave the structure similar.  You say you want to use minimization and repacking; you probably want regular old relax, not this tool that is a preparatory step for a particular ddg pipeline.

> 2) Why are there so many double colons? 

C++ uses a double colon to indicate namespacing.  I will rely on you to google namespacing in programming to learn about it.  Rosetta namespaces its command line options because there are thousands and it’s a good way to resolve name conflicts.  Double or single colons are permitted for command line flag namespacing.  I assume we allow both because some people wanted singular for compactness, and others used double because they were used to C++ and it was easier to allow both.  (It isn’t because the underlying code requires colons because it is C++, it’s just a case of progammers using familiar patterns.)

[Anonymous]

Thank you so much!! That clears up a lot of stuff. I will also besure ot check out the Meiler lab stuff

 

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