[modeller_usage] Fwd: muti template problem

# Homology modeling with multiple templates
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output
env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

a = automodel(env,
              alnfile = 'align-multiple.ali', # alignment filename
              knowns   = ('2hyd', '3g5u'),     # codes of the templates
              sequence = 'pgp_ref')               # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model = 1                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual homology modeling

C; A multiple alignment in the PIR format;

>P1;2hyd
structureX:2hyd:1: A:578 :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19
----------------------------------MIKRYLQFVKPYKYRIFATIIVGIIKFGIPMLIPLLIKYAIDGVIN
------------NHALTTDEKVHHLTIAIGIALFIFVIVRP-----PIEFIRQYLAQWTSNKILYDIRKKLYNHLQALSA
RFYANNQVGQVISRVINDVEQTKDFILTGLMNIWLDCITIFGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILSSFT
DKELHAYAKAQGFLHERVQGISVVKSFAIEDNEAKNFDKKNTNFLTRALKHTRWNAYSFAAINTVTDIGPIIVIGVGAYL
AISGSITVGTLAAFVGYLELLFGPLRRLVASFTTLTQSFASMDRVFQLIDEDYDIKNG-VGAQPIEIKQGRIDIDHVSFQ
YND-NEAPILKDINLSIEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGHNIKDFLTGSLRNQIGLVQQDNILF
SDTVKENILLGRPTATDEEV VEAAKMANAHDFIMNLPQGYDTEVGERGVKLSGGQKQRLSIARIFLNNPPILILDEATS
ALDLESESIIQEALDVLSKDRTTLIVAHRLSTITHADKIVV IENGHIVETGTHRELIAKQGAYEHLYSIQNL-------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
----------*

>P1;3g5u
structureX:3g5u:1:A: 1271 :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00
MELEEDLKGRADK-NFSKMGKKSKKEKKEKKPAVSVLTMFRYAGWLDRLY MLVGTLAAIIHGVALPLMMLIFGDMTDSF
ASVGNVS---KNSTNMSEADK RAMFAKLEEEMTTYAYYYTGIGAGVLIVAYIQVSFWCLAAGRQIHKIRQKFFHAIMNQ
EIGWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQAMATF FGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILS
SFTDKELHAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNNNLEEAKRLGIKKAITANISMGAAFLLIYASYALAFWYG
TSLVISKEYSIGQVLTVFFSVLIGAFSVGQASPNIEAFANARGAAYEVFKIIDNKPSIDSFSKSGHKPDNIQGNLEFKNI
HFSYPSRKEVQILKGLNLKVKSGQTVALVGNSGCGKSTTVQLMQRLYDPLDGMVSIDGQDIRTINVRYLREIIGVVSQEP
VLFATTIAENIRYGREDVTMDEIEKAVKEANAYDFIMKLPHQFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEA
TSALDTESEAVVQAALDKAREGRTTIVIAHRLSTVRNADVIAGFDGGVIVEQGNHDELMREKGIYFKLVMTQTAGNEIEL
GNEACKSKDEIDNLDMSSKDSGSSLIRRRSTRKSICGPHDQDRKLSTKEALDEDVPPASFWRILKLNSTEWPYFVVGIFC
AIINGGLQPAFSVIFSKVVGVFTNGGPPETQRQNSNLFSLLFLILGIISFITFFLQGFTFGKAGEILTKRLRYMVFKSML
RQDVSWFDDPKNTTGALTTRLANDAAQVKGATGSRLAVIFQNIANLGTGIIISLIYGWQLTLLLLAIVPIIAIAGVVEMK
MLSGQALKDKKELEGSGKIATEAIENFRTVVSLTREQKFETMYAQSLQIPYRNAMKKAHVFGITFSFTQAMMYFSYAAAF
RFGAYLVTQQLMTFENVLLVFSAIVFGAMAVGQVSSFAPDYAKATVSASHIIRIIEKTPEIDSYSTQGLKPNMLEGNVQF
SGVVFNYPTRPSIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPMAGSVFLDGKEIKQLNVQWLRAQLGIVS
QEPILFDCSIAENIAYGDNSRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHIL
LLDEATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVIQNGKVKEHGTHQQLLAQKGIYFSMVSVQAGA
KRSYVHHHHHH*

>P1;pgp_ref
sequence:pgp_ref:1    : :1280   : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
MDLEGDRNGGAKKKNFFKLNNKSEKDKKEKKPTVSVFSMFRYSNWLDKLYMVVGTLAAIIHGAGLPLMMLVFGEMTDIFA
NAGNLEDLMSNITNRSDINDTGFFMNLEEDMTRYAYYYSGIGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEI
GWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGLSAAVWAKILSSFT
DKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRIGIKKAITANISIGAAFLLIYASYALAFWYGTTL
VLSGEYSIGQVLTVFFSVLIGAFSVGQASPSIEAFANARGAAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFS
YPSRKEVKILKGLNLKVQSGQTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLREIIGVVSQEPVLF
ATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEATSA
LDTESEAVVQVALDKARKGRTTIVIAHRLSTVRNADVIAGFDDGVIVEKGNHDELMKEKGIYFKLVTMQTAGNEVELENA
ADESKSEIDALEMSSNDSRSSLIRKRSTRRSVRGSQAQDRKLSTKEALDESIPPVSFWRIMKLNLTEWPYFVVGVFCAII
NGGLQPAFAIIFSKIIGVFTRIDDPETKRQNSNLFSLLFLALGIISFITFFLQGFTFGKAGEILTKRLRYMVFRSMLRQD
VSWFDDPKNTTGALTTRLANDAAQVKGAIGSRLAVITQNIANLGTGIIISFIYGWQLTLLLLAIVPIIAIAGVVEMKMLS
GQALKDKKELEGSGKIATEAIENFRTVVSLTQEQKFEHMYAQSLQVPYRNSLRKAHIFGITFSFTQAMMYFSYAGCFRFG
AYLVAHKLMSFEDVLLVFSAVVFGAMAVGQVSSFAPDYAKAKISAAHIIMIIEKTPLIDSYSTEGLMPNTLEGNVTFGEV
VFNYPTRPDIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPLAGKVLLDGKEIKRLNVQWLRAHLGIVSQEP
ILFDCSIAENIAYGDNSRVVSQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHILLLD
EATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVFQNGRVKEHGTHQQLLAQKGIYFSMVSVQAGTKRQ
--------*

this the log file

ate and time of compilation         : 2010/04/21 09:52:56
MODELLER executable type             : i386-w32
Job starting time (YY/MM/DD HH:MM:SS): 2010/06/16 12:26:20

openf___224_> Open           $(LIB)/restyp.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups:        2
openf___224_> Open           ${MODINSTALL9v8}/modlib/sstruc.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3234072    3158.273     3.084

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3234600    3158.789     3.085
openf___224_> Open           ${MODINSTALL9v8}/modlib/resdih.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3283200    3206.250     3.131
rdrdih__263_> Number of dihedral angle types         :        9
              Maximal number of dihedral angle optima:        3
              Dihedral angle names                   : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open           ${MODINSTALL9v8}/modlib/radii.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3292440    3215.273     3.140
openf___224_> Open           ${MODINSTALL9v8}/modlib/radii14.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open           ${MODINSTALL9v8}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf___224_> Open           ${MODINSTALL9v8}/modlib/mnch1.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/mnch2.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/mnch3.lib
openf___224_> Open           ${MODINSTALL9v8}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
openf___224_> Open           align-multiple.ali

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3303853    3226.419     3.151

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3305303    3227.835     3.152

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3308203    3230.667     3.155

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3314003    3236.331     3.160

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3325603    3247.659     3.172

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3348803    3270.315     3.194

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3800163    3711.097     3.624

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      3802479    3713.358     3.626

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      3807623    3718.382     3.631

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      3812739    3723.378     3.636
read_al_375E> Unknown residue type,position,sequence:        501        1

--
With Regards:
Shikha Agarwal
IBI2009009
IIIT-A