Hi, i generated a model using the model_single.py example. So this is without loop modeling. Now I would like to model loops only, using the example from the manual: from modeller import * from modeller.automodel import * class my_lm(dope_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('535', '562')) env = environ() a = my_lm(env, alnfile='HsMhc1_best_no_loops_motor.ali', knowns='1DFK_motor', sequence='HsMhc1') a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 5 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() Please note that I used the dope_loopmodel class instead of loopmodel as indicated in the manual. When I run the script, it exits with the following message: report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 1 68 111 445 496 671 602 791 874 924 1041 << end of ENERGY. iatmcls_286W> MODEL atom not classified: GLU:OXT GLU preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. Using dopehr_loopmodel gives the same error whereas the "old" loopmodel works. Here is the Atom record from the PDB file: ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294 The coordinates do not seem to be out of range. I also put a blank in the middle ("1.00 103.06") to avoid problems with the parser, but to no avail. Am I doing something wrong here or is this a bug? Any help on this is greatly appreciated. Florian