PDB IDs must be correctly mentioned with their considered chain Identifiers.
Good Luck
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Thursday, June 16, 2011 1:35:24 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 90
Send modeller_usage mailing list submissions to
To subscribe or unsubscribe via the World Wide Web, visit
https://salilab.org/mailman/listinfo/modeller_usage
or, via email, send a message with subject or body 'help' to
You can reach the person managing the list at
When replying, please edit your Subject line so it is more specific
than "Re: Contents of modeller_usage digest..."
Today's Topics:
1. Re: problem with mac version (Modeller Caretaker)
2. Fwd: muti template problem (shikha agarwal)
----------------------------------------------------------------------
Message: 1
Date: Wed, 08 Jun 2011 10:29:48 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] problem with mac version
To: Anthony Couvreux <>
Cc:
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 6/8/11 10:01 AM, Anthony Couvreux wrote:
> I have a "segmentation fault" message on my Imac (Mac OS X version 10.5.8).
> Even using files that worked successfully on PC.
> Does any relation with my Mac configuration? Installedversion of
> Python is 2.5.1.
See http://salilab.org/modeller/9.9/manual/node10.html
Without seeing your input files or any more particulars (e.g. does it
crash immediately or partway through the run, what version of Modeller
are you using, etc.) it is essentially impossible to help you further.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 2
Date: Thu, 16 Jun 2011 13:35:22 +0530
From: shikha agarwal <>
Subject: [modeller_usage] Fwd: muti template problem
To:
Message-ID: <BANLkTikpBOx-Hg=>
Content-Type: text/plain; charset="iso-8859-1"
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://salilab.org/archives/modeller_usage/attachments/20110616/97239bc2/attachment.html
------------------------------
_______________________________________________
modeller_usage mailing list
https://salilab.org/mailman/listinfo/modeller_usage
End of modeller_usage Digest, Vol 10, Issue 90
**********************************************