Dear Modeller,

I have been trying to include some hetatms in my models but so far all that seems to appear apart from the main chain is a few characters at the end of the modelled sequence.  I know that there must be something obvious that I am doing wrong but cannot for the life of me work out what it is!

I have modified the PDBs 2Z7X, 2Z80, 2Z82 and 3A79 to include only the chain of interest (using PyMOL) and only in 2Z7X have I kept the HETATMs of interest.  I have copied in my script and alignment below. 

Any help that can be offered would be so very much appreciated!

Best wishes,

Tory

from modeller import *

from modeller.automodel import *

log.verbose()

env = environ()

env.io.atom_files_directory = ['/home/tory/data/bTLR2_april12/PDBs/']

env.io.hetatm = True

a = automodel(env,

                                                                alnfile='../modeller_alignment_with_glyc_pir_format.ali',

                knowns=('2Z7XchainA','2Z82chainA','3A7BchainA','2Z80chainB'), sequence='btau-tlr2',

                assess_methods=(assess.DOPE, assess.normalized_dope, assess.DOPEHR, assess.GA341))

a.starting_model = 1

a.ending_model = 50

# Very thorough VTFM optimization:

a.library_schedule = autosched.slow

a.max_var_iterations = 300

# Thorough MD optimization:

a.md_level = refine.slow

# Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6

a.repeat_optimization = 5

a.max_molpdf = 1e6

a.make()

>P1;2Z82chainA

structureX:2Z82chainA::A:548:A:TLR2:mus musculus:2.60:0.22

-SLSCDASGVCDGRSRSFTSIPSGLTAAMKSLDLSFNKITYIGHGDLRACANLQVLILKS

SRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLF

PNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTL

HLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDES

FNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLF

YDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGA

WPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSS

TGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMK

ISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW----*

>P1;3A7BchainA

structureX:3A7BchainA::A::A:TLR2:mus musculus:2.53:0.24

ESLSCDASGVCDGRSRSFTSIPSGLTAAMKSLDLSFNKITYIGHGDLRACANLQVLILKS

SRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLF

PNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTL

HLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDES

FNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLF

YDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGA

WPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSS

TGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMK

IASNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW----*

>P1;2Z7XchainA

structureX:2Z7XchainA:27:A:::TLR2:homo sapiens:2.10:0.24

-SLSCDRNGICKGSSGSLNSIPSGLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTS

NGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLF

SHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLIL

HMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDES

LFQVMKLLNQISGLLELEFDDCTLNGVGNFRASDNDRVIDPGKVETLTIRRLHIPRFYLF

YDLSTLYSLTERVKRITVENSKVFLVPCLLSQHLKSLEYLDLSENLMVEEYLKNSACEDA

WPSLQTLILRQNHLASLEKTGETLLTLKNLTNIDISKNSFHSMPETCQWPEKMKYLNLSS

TRIHSVTGCIPKTLEILDVSNNNLNLFSLNLPQLKELYISRNKLMTLPDASLLPMLLVLK

ISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW....*

>P1;2Z80chainB

structureX:2Z80chainB::B::B:TLR2:homo sapiens:1.80:0.22

-SLSCDRNGICKGSSGSLNSIPSGLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTS

NGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLF

SHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLIL

HMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFS-------NSLIKKFTFRNVKITDES

LFQVMKLLNQISG-----------------------------------------------

------------------------------------------------------------

------------------------------------------------------------

------------------------------------------------------------

----------------------------------------------*

>P1;btau-tlr2

sequence:btau-tlr2:::::TLR2:bovine AAL16722|AF368419:2.00:-1.00

SSLSCDPTGVCDGHSRSLNSIPSGLTAGVKSLDLSNNDITYVGNRDLQRCVNLKTLRLGA

NEIHTVEEDSFFHLRNLEYLDLSYNRLSNLSSSWFRSLYVLKFLNLLGNLYKTLGETSLF

SHLPNLRTLKVGNSNSFTEIHEKDFTGLTFLEELEISAQNLQIYVPKSLKSIQNISHLIL

HLKQPILLVDILVDIVSSLDCFELRDTNLHTFHFSEASISEMSTSVKKLIFRNVQFTDES

FVEVVKLFNYVSGILEVEFDDCTHDGIGDFRALSLDRIRHLGNVETLTIRKLHIPQFFLF

HDLSSIYPLTGRVKRVTIENSKVFLVPCLLSQHLKSLEYLDLSENLMSEETLKNSACKDA

WPFLQTLVLRQNRLKSLEKTGELLLTLENLNNLDISKNNFLSMPETCQWPGKMKQLNLSS

TRIHSLTQCLPQTLEILDVSNNNLDSFSLILPQLKELYISRNKLKTLPDASFLPVLSVMR

ISRNIINTFSKEQLDSFQQLKTLEAGGNNFICSCDFLSFTQGQ....*