Hello
while performing the modellin using multitemplate I am facing problem . the model-multiple.py , align.ali and generated log files are pasted below . plz help memodel-multiple.py file
# 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
--
With Regards:
Shikha Agarwal
IBI2009009
IIIT-A