[modeller_usage] not generating pdb files

Hi,

I'm running modeller 8v0, and am trying to model 2 different proteins on the
same template.  For some reason, for one of the alignments (#1), the only output
being produced is the .D* and .V* files - the models aren't being generated (and
the D* and V* files are being produced quite quickly).
For alignment #2, I'm getting the models out so that isn't a problem.

Any help would be appreciated...the same commands are being used for both
alignments, which i've shown below..

Gerald

------------
script command:

def my_model(_alnfile, _knowns, _sequence):
        log.verbose() #request verbose output

        env = environ() #create a new MODELLER environment to build model

        env.io.atom_files_directory = './:../pdb/'

        a = automodel (env, alnfile = _alnfile, knowns = _knowns, sequence =
_sequence)
        a.starting_model = 1
        a.ending_model = 50
        a.final_malign3d = True
        a.md_level = refine.slow

        a.make()

-----------
alignment #1:
>P1;1PVM
structureX:1PVM:FIRST:A:LAST :B:.:.: 0.00: 0.00
KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE
RSIIKRFIPRNKKPDEV-------------------------------------------
------------------------------------------------------------
-----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY
LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS/
KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE
RSIIKRFIPRNKKPDEV-------------------------------------------
------------------------------------------------------------
-----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY
LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS
*
>P1;a1
sequence::     : :     : :::-1.00:-1.00
DIMVRDVPHVALS-CTFRDLRLALHRTK--GRMLALVES--P---ESMI----LLGSIER
SQVVALLGAQLSPARRRQHMQERRATQTSPLSDQEGPPSPEASVCFQVNTEDSAFPAARG
ETHKPLKPALKRGPSVTRNLGESPTGSAESAGIALRSLFCGSPPPEAASEKLESCEKRKL
KRVRISLASDADLEGEMSPEEILEWEEQQLDEPVNFSDCKIDPAPFQLVERTSLHKTHTI
FSLLGVDHAYVT-SIGRLIGIVTLKELRKAIE/
DIMVRDVPHVALS-CTFRDLRLALHRTK--GRMLALVES--P---ESMI----LLGSIER
SQVVALLGAQLSPARRRQHMQERRATQTSPLSDQEGPPSPEASVCFQVNTEDSAFPAARG
ETHKPLKPALKRGPSVTRNLGESPTGSAESAGIALRSLFCGSPPPEAASEKLESCEKRKL
KRVRISLASDADLEGEMSPEEILEWEEQQLDEPVNFSDCKIDPAPFQLVERTSLHKTHTI
FSLLGVDHAYVT-SIGRLIGIVTLKELRKAIE
*


------------------------------
Alignment #2:

>P1;1PVM
structureX:1PVM:FIRST:A:LAST :B:.:.: 0.00: 0.00
KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE
RSIIKRFIPRNKKPDEV-------------------------------------------
------------------------------------------------------------
-----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY
LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS/
KIMNSNFKTVNWN-TTVFDAVKIMNENH----LYGLVVK--D---DNGN----DVGLLSE
RSIIKRFIPRNKKPDEV-------------------------------------------
------------------------------------------------------------
-----------------------------------PIRLVMRKPIPKVKSDYDVKDVAAY
LSENGLERCAVVDDPGRVVGIVTLTDLSRYLS
*
>P1;a2
sequence::     : :     : :::-1.00:-1.00
RRNDPLLTVLTQDSMTVEDVETIISETT--YSGFPVVVS--R---ESQR----LVGFVLR
RDLIISIENARKKQDGVV------------------------------------------
------------------------------------------------------------
-------------STSIIYFTEHSPPLPPYTPPTLKLRNILDLSPFTVTDLTPMEIVVDI
FRKLGLRQCLVT-HNGRLLGIITKKDVLKHIA/
RRNDPLLTVLTQDSMTVEDVETIISETT--YSGFPVVVS--R---ESQR----LVGFVLR
RDLIISIENARKKQDGVV------------------------------------------
------------------------------------------------------------
-------------STSIIYFTEHSPPLPPYTPPTLKLRNILDLSPFTVTDLTPMEIVVDI
FRKLGLRQCLVT-HNGRLLGIITKKDVLKHIA
*