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Side chain sampling

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Side chain sampling

I need to use rosetta for proteins for side-chain sampling keeping the backbone fixed.
I tried using the fixed-backbone-design module by specifying the residues with the fixed backbone, but the method does the side-chain sampling using some preferred discrete rotamers.
Is there some way I can do the thorough sampling of side chains using MC optimizations (which could be more compute intensive) and not using the discrete rotamers?

Wed, 2009-04-15 10:14

you may want to try using the mcmin_trials option.

Additionally you can expand the rotamer set using the -ex options

for example

-ex1 7

adds rotamers with chi1 angles sampled in six quarter standard deviation steps

see the README for a little more description.

Tue, 2009-04-21 15:32