<br>Hello <br><br><br>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<br><div class="gmail_quote">
<br># Homology modeling with multiple templates<br>from modeller import * # Load standard Modeller classes<br>from modeller.automodel import * # Load the automodel class<br><br>log.verbose() # request verbose output<br>
env = environ() # create a new MODELLER environment to build this model in<br><br># directories for input atom files<br>env.io.atom_files_directory = ['.', '../atom_files']<br><br>a = automodel(env,<br> alnfile = 'align-multiple.ali', # alignment filename<br>
knowns = ('2hyd', '3g5u'), # codes of the templates<br> sequence = 'pgp_ref') # code of the target<br>a.starting_model= 1 # index of the first model<br>
a.ending_model = 1 # index of the last model<br> # (determines how many models to calculate)<br>a.make() # do the actual homology modeling<br>
<br><br><br>C; A multiple alignment in the PIR format; <br><br>>P1;2hyd<br>structureX:2hyd:1: A:578 :A:ferredoxin:Azotobacter vinelandii: 1.90: 0.19<br>----------------------------------MIKRYLQFVKPYKYRIFATIIVGIIKFGIPMLIPLLIKYAIDGVIN<br>
------------NHALTTDEKVHHLTIAIGIALFIFVIVRP-----PIEFIRQYLAQWTSNKILYDIRKKLYNHLQALSA<br>RFYANNQVGQVISRVINDVEQTKDFILTGLMNIWLDCITIFGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILSSFT<br>DKELHAYAKAQGFLHERVQGISVVKSFAIEDNEAKNFDKKNTNFLTRALKHTRWNAYSFAAINTVTDIGPIIVIGVGAYL<br>
AISGSITVGTLAAFVGYLELLFGPLRRLVASFTTLTQSFASMDRVFQLIDEDYDIKNG-VGAQPIEIKQGRIDIDHVSFQ<br>YND-NEAPILKDINLSIEKGETVAFVGMSGGGKSTLINLIPRFYDVTSGQILIDGHNIKDFLTGSLRNQIGLVQQDNILF<br>SDTVKENILLGRPTATDEEV VEAAKMANAHDFIMNLPQGYDTEVGERGVKLSGGQKQRLSIARIFLNNPPILILDEATS<br>
ALDLESESIIQEALDVLSKDRTTLIVAHRLSTITHADKIVV IENGHIVETGTHRELIAKQGAYEHLYSIQNL-------<br>--------------------------------------------------------------------------------<br>--------------------------------------------------------------------------------<br>
--------------------------------------------------------------------------------<br>--------------------------------------------------------------------------------<br>--------------------------------------------------------------------------------<br>
--------------------------------------------------------------------------------<br>--------------------------------------------------------------------------------<br>--------------------------------------------------------------------------------<br>
----------*<br><br>>P1;3g5u<br>structureX:3g5u:1:A: 1271 :A:ferredoxin:Bacillus schlegelii:-1.00:-1.00<br>MELEEDLKGRADK-NFSKMGKKSKKEKKEKKPAVSVLTMFRYAGWLDRLY MLVGTLAAIIHGVALPLMMLIFGDMTDSF<br>ASVGNVS---KNSTNMSEADK RAMFAKLEEEMTTYAYYYTGIGAGVLIVAYIQVSFWCLAAGRQIHKIRQKFFHAIMNQ<br>
EIGWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQAMATF FGGFIIGFTRGWKLTLVILAISPVLGLSAGIWAKILS<br>SFTDKELHAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNNNLEEAKRLGIKKAITANISMGAAFLLIYASYALAFWYG<br>TSLVISKEYSIGQVLTVFFSVLIGAFSVGQASPNIEAFANARGAAYEVFKIIDNKPSIDSFSKSGHKPDNIQGNLEFKNI<br>
HFSYPSRKEVQILKGLNLKVKSGQTVALVGNSGCGKSTTVQLMQRLYDPLDGMVSIDGQDIRTINVRYLREIIGVVSQEP<br>VLFATTIAENIRYGREDVTMDEIEKAVKEANAYDFIMKLPHQFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEA<br>TSALDTESEAVVQAALDKAREGRTTIVIAHRLSTVRNADVIAGFDGGVIVEQGNHDELMREKGIYFKLVMTQTAGNEIEL<br>
GNEACKSKDEIDNLDMSSKDSGSSLIRRRSTRKSICGPHDQDRKLSTKEALDEDVPPASFWRILKLNSTEWPYFVVGIFC<br>AIINGGLQPAFSVIFSKVVGVFTNGGPPETQRQNSNLFSLLFLILGIISFITFFLQGFTFGKAGEILTKRLRYMVFKSML<br>RQDVSWFDDPKNTTGALTTRLANDAAQVKGATGSRLAVIFQNIANLGTGIIISLIYGWQLTLLLLAIVPIIAIAGVVEMK<br>
MLSGQALKDKKELEGSGKIATEAIENFRTVVSLTREQKFETMYAQSLQIPYRNAMKKAHVFGITFSFTQAMMYFSYAAAF<br>RFGAYLVTQQLMTFENVLLVFSAIVFGAMAVGQVSSFAPDYAKATVSASHIIRIIEKTPEIDSYSTQGLKPNMLEGNVQF<br>SGVVFNYPTRPSIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPMAGSVFLDGKEIKQLNVQWLRAQLGIVS<br>
QEPILFDCSIAENIAYGDNSRVVSYEEIVRAAKEANIHQFIDSLPDKYNTRVGDKGTQLSGGQKQRIAIARALVRQPHIL<br>LLDEATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVIQNGKVKEHGTHQQLLAQKGIYFSMVSVQAGA<br>KRSYVHHHHHH*<br><br>>P1;pgp_ref<br>sequence:pgp_ref:1 : :1280 : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00<br>
MDLEGDRNGGAKKKNFFKLNNKSEKDKKEKKPTVSVFSMFRYSNWLDKLYMVVGTLAAIIHGAGLPLMMLVFGEMTDIFA<br>NAGNLEDLMSNITNRSDINDTGFFMNLEEDMTRYAYYYSGIGAGVLVAAYIQVSFWCLAAGRQIHKIRKQFFHAIMRQEI<br>GWFDVHDVGELNTRLTDDVSKINEGIGDKIGMFFQSMATFFTGFIVGFTRGWKLTLVILAISPVLGLSAAVWAKILSSFT<br>
DKELLAYAKAGAVAEEVLAAIRTVIAFGGQKKELERYNKNLEEAKRIGIKKAITANISIGAAFLLIYASYALAFWYGTTL<br>VLSGEYSIGQVLTVFFSVLIGAFSVGQASPSIEAFANARGAAYEIFKIIDNKPSIDSYSKSGHKPDNIKGNLEFRNVHFS<br>YPSRKEVKILKGLNLKVQSGQTVALVGNSGCGKSTTVQLMQRLYDPTEGMVSVDGQDIRTINVRFLREIIGVVSQEPVLF<br>
ATTIAENIRYGRENVTMDEIEKAVKEANAYDFIMKLPHKFDTLVGERGAQLSGGQKQRIAIARALVRNPKILLLDEATSA<br>LDTESEAVVQVALDKARKGRTTIVIAHRLSTVRNADVIAGFDDGVIVEKGNHDELMKEKGIYFKLVTMQTAGNEVELENA<br>ADESKSEIDALEMSSNDSRSSLIRKRSTRRSVRGSQAQDRKLSTKEALDESIPPVSFWRIMKLNLTEWPYFVVGVFCAII<br>
NGGLQPAFAIIFSKIIGVFTRIDDPETKRQNSNLFSLLFLALGIISFITFFLQGFTFGKAGEILTKRLRYMVFRSMLRQD<br>VSWFDDPKNTTGALTTRLANDAAQVKGAIGSRLAVITQNIANLGTGIIISFIYGWQLTLLLLAIVPIIAIAGVVEMKMLS<br>GQALKDKKELEGSGKIATEAIENFRTVVSLTQEQKFEHMYAQSLQVPYRNSLRKAHIFGITFSFTQAMMYFSYAGCFRFG<br>
AYLVAHKLMSFEDVLLVFSAVVFGAMAVGQVSSFAPDYAKAKISAAHIIMIIEKTPLIDSYSTEGLMPNTLEGNVTFGEV<br>VFNYPTRPDIPVLQGLSLEVKKGQTLALVGSSGCGKSTVVQLLERFYDPLAGKVLLDGKEIKRLNVQWLRAHLGIVSQEP<br>ILFDCSIAENIAYGDNSRVVSQEEIVRAAKEANIHAFIESLPNKYSTKVGDKGTQLSGGQKQRIAIARALVRQPHILLLD<br>
EATSALDTESEKVVQEALDKAREGRTCIVIAHRLSTIQNADLIVVFQNGRVKEHGTHQQLLAQKGIYFSMVSVQAGTKRQ<br>--------*<br><br><br><br><br><br><br>this the log file <br><br><br>ate and time of compilation : 2010/04/21 09:52:56<br>MODELLER executable type : i386-w32<br>
Job starting time (YY/MM/DD HH:MM:SS): 2010/06/16 12:26:20<br><br>openf___224_> Open $(LIB)/restyp.lib<br>openf___224_> Open ${MODINSTALL9v8}/modlib/resgrp.lib<br>rdresgr_266_> Number of residue groups: 2<br>
openf___224_> Open ${MODINSTALL9v8}/modlib/sstruc.lib<br><br>Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234072 3158.273 3.084<br><br>Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3234600 3158.789 3.085<br>
openf___224_> Open ${MODINSTALL9v8}/modlib/resdih.lib<br><br>Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3283200 3206.250 3.131<br>rdrdih__263_> Number of dihedral angle types : 9<br>
Maximal number of dihedral angle optima: 3<br> Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5<br>openf___224_> Open ${MODINSTALL9v8}/modlib/radii.lib<br>
<br>Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 3292440 3215.273 3.140<br>openf___224_> Open ${MODINSTALL9v8}/modlib/radii14.lib<br>openf___224_> Open ${MODINSTALL9v8}/modlib/af_mnchdef.lib<br>
rdwilmo_274_> Mainchain residue conformation classes: APBLE<br>openf___224_> Open ${MODINSTALL9v8}/modlib/mnch.lib<br>rdclass_257_> Number of classes: 5<br>openf___224_> Open ${MODINSTALL9v8}/modlib/mnch1.lib<br>
openf___224_> Open ${MODINSTALL9v8}/modlib/mnch2.lib<br>openf___224_> Open ${MODINSTALL9v8}/modlib/mnch3.lib<br>openf___224_> Open ${MODINSTALL9v8}/modlib/xs4.mat<br>rdrrwgh_268_> Number of residue types: 21<br>
openf___224_> Open align-multiple.ali<br><br>Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3303853 3226.419 3.151<br><br>Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3305303 3227.835 3.152<br>
<br>Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3308203 3230.667 3.155<br><br>Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3314003 3236.331 3.160<br><br>Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3325603 3247.659 3.172<br>
<br>Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3348803 3270.315 3.194<br><br>Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 3800163 3711.097 3.624<br><br>Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3802479 3713.358 3.626<br>
<br>Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3807623 3718.382 3.631<br><br>Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 3812739 3723.378 3.636<br>read_al_375E> Unknown residue type,position,sequence: 501 1<br>
<font color="#888888">
<br clear="all"><br>-- <br>With Regards:<br>Shikha Agarwal<br>IBI2009009<br>IIIT-A<br><br>
</font></div><br><br clear="all"><br>-- <br>With Regards:<br>Shikha Agarwal<br>IBI2009009<br>IIIT-A<br><br>