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<p class="MsoNormal"><span style="color:#1F497D">Hi Tory,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">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”<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Hope this helps<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">J<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org]
<b>On Behalf Of </b>Offord, Victoria<br>
<b>Sent:</b> Friday, 27 April 2012 1:55 a.m.<br>
<b>To:</b> 'modeller_usage@salilab.org'<br>
<b>Subject:</b> [modeller_usage] modelling with hetatms<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="EN-GB">Dear Modeller,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">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!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">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.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Any help that can be offered would be so very much appreciated!<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Tory<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">from modeller import *<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">from modeller.automodel import *<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">log.verbose()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">env = environ()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">env.io.atom_files_directory = ['/home/tory/data/bTLR2_april12/PDBs/']<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">env.io.hetatm = True<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a = automodel(env, <o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"> alnfile='../modeller_alignment_with_glyc_pir_format.ali',<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"> knowns=('2Z7XchainA','2Z82chainA','3A7BchainA','2Z80chainB'), sequence='btau-tlr2',<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"> assess_methods=(assess.DOPE, assess.normalized_dope, assess.DOPEHR, assess.GA341))<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a.starting_model = 1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a.ending_model = 50<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"># Very thorough VTFM optimization:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a.library_schedule = autosched.slow<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a.max_var_iterations = 300<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"># Thorough MD optimization:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a.md_level = refine.slow<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"># Repeat the whole cycle 2 times and do not stop unless obj.func. > 1E6<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a.repeat_optimization = 5<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a.max_molpdf = 1e6<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">a.make()<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">>P1;2Z82chainA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">structureX:2Z82chainA::A:548:A:TLR2:mus musculus:2.60:0.22<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">-SLSCDASGVCDGRSRSFTSIPSGLTAAMKSLDLSFNKITYIGHGDLRACANLQVLILKS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">SRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">PNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTL<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">HLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDES<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">FNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">YDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">WPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">TGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMK<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">ISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW----*<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">>P1;3A7BchainA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">structureX:3A7BchainA::A::A:TLR2:mus musculus:2.53:0.24<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">ESLSCDASGVCDGRSRSFTSIPSGLTAAMKSLDLSFNKITYIGHGDLRACANLQVLILKS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">SRINTIEGDAFYSLGSLEHLDLSDNHLSSLSSSWFGPLSSLKYLNLMGNPYQTLGVTSLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">PNLTNLQTLRIGNVETFSEIRRIDFAGLTSLNELEIKALSLRNYQSQSLKSIRDIHHLTL<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">HLSESAFLLEIFADILSSVRYLELRDTNLARFQFSPLPVDEVSSPMKKLAFRGSVLTDES<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">FNELLKLLRYILELSEVEFDDCTLNGLGDFNPSESDVVSELGKVETVTIRRLHIPQFYLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">YDLSTVYSLLEKVKRITVENSKVFLVPCSFSQHLKSLEFLDLSENLMVEEYLKNSACKGA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">WPSLQTLVLSQNHLRSMQKTGEILLTLKNLTSLDISRNTFHPMPDSCQWPEKMRFLNLSS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">TGIRVVKTCIPQTLEVLDVSNNNLDSFSLFLPRLQELYISRNKLKTLPDASLFPVLLVMK<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">IASNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW----*<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">>P1;2Z7XchainA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">structureX:2Z7XchainA:27:A:::TLR2:homo sapiens:2.10:0.24<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">-SLSCDRNGICKGSSGSLNSIPSGLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">NGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">SHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLIL<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">HMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFSELSTGETNSLIKKFTFRNVKITDES<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">LFQVMKLLNQISGLLELEFDDCTLNGVGNFRASDNDRVIDPGKVETLTIRRLHIPRFYLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">YDLSTLYSLTERVKRITVENSKVFLVPCLLSQHLKSLEYLDLSENLMVEEYLKNSACEDA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">WPSLQTLILRQNHLASLEKTGETLLTLKNLTNIDISKNSFHSMPETCQWPEKMKYLNLSS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">TRIHSVTGCIPKTLEILDVSNNNLNLFSLNLPQLKELYISRNKLMTLPDASLLPMLLVLK<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">ISRNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRW....*<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">>P1;2Z80chainB<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">structureX:2Z80chainB::B::B:TLR2:homo sapiens:1.80:0.22<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">-SLSCDRNGICKGSSGSLNSIPSGLTEAVKSLDLSNNRITYISNSDLQRCVNLQALVLTS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">NGINTIEEDSFSSLGSLEHLDLSYNYLSNLSSSWFKPLSSLTFLNLLGNPYKTLGETSLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">SHLTKLQILRVGNMDTFTKIQRKDFAGLTFLEELEIDASDLQSYEPKSLKSIQNVSHLIL<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">HMKQHILLLEIFVDVTSSVECLELRDTDLDTFHFS-------NSLIKKFTFRNVKITDES<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">LFQVMKLLNQISG-----------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">----------------------------------------------*<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">>P1;btau-tlr2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">sequence:btau-tlr2:::::TLR2:bovine AAL16722|AF368419:2.00:-1.00<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">SSLSCDPTGVCDGHSRSLNSIPSGLTAGVKSLDLSNNDITYVGNRDLQRCVNLKTLRLGA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">NEIHTVEEDSFFHLRNLEYLDLSYNRLSNLSSSWFRSLYVLKFLNLLGNLYKTLGETSLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">SHLPNLRTLKVGNSNSFTEIHEKDFTGLTFLEELEISAQNLQIYVPKSLKSIQNISHLIL<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">HLKQPILLVDILVDIVSSLDCFELRDTNLHTFHFSEASISEMSTSVKKLIFRNVQFTDES<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">FVEVVKLFNYVSGILEVEFDDCTHDGIGDFRALSLDRIRHLGNVETLTIRKLHIPQFFLF<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">HDLSSIYPLTGRVKRVTIENSKVFLVPCLLSQHLKSLEYLDLSENLMSEETLKNSACKDA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">WPFLQTLVLRQNRLKSLEKTGELLLTLENLNNLDISKNNFLSMPETCQWPGKMKQLNLSS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">TRIHSLTQCLPQTLEILDVSNNNLDSFSLILPQLKELYISRNKLKTLPDASFLPVLSVMR<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">ISRNIINTFSKEQLDSFQQLKTLEAGGNNFICSCDFLSFTQGQ....*<o:p></o:p></span></p>
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