[modeller_usage] Error when using flex-em

[Saskia Bakker <>]

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
  File "/fbs/emdisk3/emsoftware/LINUX/modeller9v7/modlib/modeller/optimizers/molecular_dynamics.py",
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
(usually infinity).
              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
enough).
I would be very grateful for any suggestions to help solve this problem.

Many thanks,

Saskia