I have finished the fragmentation step using CS-Rosetta (with file aa_t000.xx03xx.v_3 and aa_t000.xx09xx.v_3). Now I want to generate protein structures from them and meanwhile apply NOE distance constraints. I have tried to only build 1 structural model. The resulting pdb structure does not satisfy the NOE constraint. I have the following questions:
(1) what is the appropriate way to check the NOE distance constraints have been applied? In other words, is my expectation (the NOE constraint should be there even though only one model has been generated) right?
(2) what else is needed to be done in addition to have the –cst cst flag in order to apply the constraint for Rosetta 2.3.1?
• For example, will the option “-abrelax” just ignore the constraint introduced by “-cst”
(3) how could I achieve my goal in Rosetta 3.1? what is the current status of Rosetta 3.1 for the above mentioned task.
Any inputs and comments would be highly appreciated.
Many Thanks,
Lucy
I can't answer your questions fully; hopefully someone else will come along who will.
A) As general rule, nothing in Rosetta is intended to be done as a "make one model and you're done" experiment, because Rosetta uses Monte Carlo sampling instead of something more deterministic that looks for a GMEC. Minimum runs for fixed backbone design should be in the hundreds of trajectories and for flexible backbone anything probably in the high thousands and up. So, it's entirely possible the code is working right, and you've used it right, you just got unlucky with Monte Carlo.
B) I don't know what else is needed in 2.3.1, but I would expect that the score result for the trajectory should include the constraint score if constraints were working. Look for a scorefunction term in the score results that has cst or constraint in it?
C) I don't think the NOE stuff made it into 3.1. I think it will make it into 3.2 which is due any day now.
Smlewis,
Thank you very much for your comment! Everything is making sense now.
Lucy