Hi list,
As a first step towards a serious usage of IMP, I tried to write a sample code using rigid bodies, restraints and optimizers.
With MonteCarlo optimizer, at the end of optimization the model seems to remains unchanged. With ConjugateGradients or SteepestDescent, when using too many steps in the optimizer (under 100 though !?) the script generally crashes with one of these error messages :
File "/usr/local/lib/python2.6/site-packages/IMP/core/__init__.py", line 642, in optimize
def optimize(self, *args): return _IMP_core.ConjugateGradients_optimize(self, *args)
_IMP.UsageException: Attempting to construct a rotation from a non-quaternion value. The coefficient vector must have a length of 1. Got: 0.165858 -0.916284 0.55176 0.327904 gives 1.27905
File "/usr/local/lib/python2.6/site-packages/IMP/core/__init__.py", line 642, in optimize
def optimize(self, *args): return _IMP_core.ConjugateGradients_optimize(self, *args)
_IMP.UsageException: Attempting to construct a rotation from a non-quaternion value. The coefficient vector must have a length of 1. Got: 0.389486 -0.600546 0.553302 0.99031 gives 1.79921
Moreover when the script finishes, its outputs seem not relevant at all, though the score is better (smaller). maybe it is normal though, due to the choice of my restraints or to the lack of optimization steps… I think my understanding of IMP usage is still very far from perfect, will you help me sorting that out by having a look at my code ?
You will fin the script attached to this message, its outlet is really basic :
- a structure is loaded ( I choose 1RDT, a complex comprising two protein domains and two peptides)
- a map is sampled at 10A for that structure
- chains are extracted from the structure, rigidified and randomly moved in space
- two restraints are added to the model in order to tale into account
- the fit of all atoms to the sampled map
- no steric clashes between rigid bodies
- optimization
thank you very much
Dr. Benjamin SCHWARZ
Biocomputing group
Voice : +33 (0)3 68 85 47 30
FAX : +33 (0)3 68 85 47 18
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