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Snugdock and antibody modelling

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Snugdock and antibody modelling

Hi all,

I'm using version 3.1. I'm a bit confused about if snugdock and antibody modelling can be done in 3.1. both mention the command rosetta.gcc which I don't seem to have.

-is snugdock an option in the docking_protocol.linuxgccrelease? Or is snugdock to be downloaded separately and installed to be used with 3.1?

-what command is used for antibody modelling in 3.1?

-after generating say 10000 structures, how can I sort the results based on the rms and total score (here I'd be comparing with the native complex, so I assume I can take the decoy with the least rms).

many thanks in advance.

p.s. Thanks again to smlewis for posting the answer again to an earlier question.

Thu, 2010-06-10 08:13

I don't believe the antibody stuff was released in 3.1. I think you need to use 2.3 (which passes everything through the monolithic rosetta.gcc). There is antibody stuff within 3.1 down in the libraries, but the executeable wasn't released.

I'm assuming you're using *nix; the easiest way to sort your results is...sort.

sort -n -k2 score.fasc

will sort based on the second column (which is usually total_score); you can also sort on RMSD. There may be scripts available for making score versus RMSD plots; there's also a pymol plotter (src/rdwizard/rmsd_score_pymol_plotter) which creates RMSD/score plots in pymol where you can click on a point and it loads that structure.

Fri, 2010-06-11 07:29