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Re: [modeller_usage] Distance restraint violations

On 01/02/2017 08:08 AM, Albers, Thomas wrote:
I'm trying to model a certain membrane protein. There are two template
structures with decent sequence similariry (~ 40 %) and not-so-great
resolution (~ 3 angstrom).

When building a model against either template nothing in particular
sticks out in the logfile, but when building a model model against both
templates combined there are lots of distance violations (CA-CA and N-O)
in the log, however this model gives the lowest DOPE score.

This sounds reasonable. When you have two templates, you're going to have lots of bimodal restraints. When one template says a given distance is 10A and the other says 20A, Modeller doesn't restrain that distance to 15A, but to either of those two minima. So whichever one it picks the other will be violated.

DOPE scores the model on it being "native protein like" without taking the templates into account, so those violations aren't going to bother it.

	Ben Webb, Modeller Caretaker
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage