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 *