[modeller_usage] Error when using dope_loopmodel

[Florian Odronitz <>]

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