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Hi Tory, On a quick glance, I am assuming you want to keep the sugars. You can specify which ones they are instead of using a generic “.” E.g. Mannose is 2 Look in C:\Program Files (x86)\Modeller9.10\modlib\restyp_accelrys.lib
for the full list. Also there may some over-riding issue that excludes them as they are only in one template. Maybe you need to include a “.” Before the dashes at the end other sequences e.g. SRW.----, this to me indicates a break
of the chain and more residues “expected” Hope this helps J From: [mailto:]
On Behalf Of Offord, Victoria 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....* |