Dear Modeller support,
When trying to fit the crystal structure in an EM map using mod9v7 and
the flex-em script (unmodified apart from filenames) I get the
following error message:
bash $> /usr/bin/python ../../scripts/flex-em.py > flex.log
line 50, in optimize
ret = func(self._modpt, mdl.modpt, edat.modpt, libs.modpt, inds, **vars)
OverflowError: check_inf__E> Atom 1 has out-of-range coordinates
The objective function can thus not be calculated.
It happens when running in CG mode and MD mode. The map is 140x140x140
pixels, which is already 1/8 of the complete map (using the complete
map gives the exact same error). There are 893 residues (6 rigid body
domains) in the model I am trying to fit. It gives the same error with
poly-Ala. Are these files too large?
The coordinates of the pdb files that are output after the first
iteration look sensible and fit well in the map (but not quite well
I would be very grateful for any suggestions to help solve this problem.