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....*
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: modeller_usage-bounces@salilab.org [mailto:modeller_usage-bounces@salilab.org] On Behalf Of Offord, Victoria Sent: Friday, 27 April 2012 1:55 a.m. To: 'modeller_usage@salilab.org' Subject: [modeller_usage] modelling with hetatms
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....*
On 04/26/2012 06:54 AM, Offord, Victoria wrote: > 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!
Your alignment file and Python script look fine to me. What happens when you run it?
Ben Webb, Modeller Caretaker
Apparently, I was being a little daft and forgot I needed to use the full template sequence prior to the ligand! It seems to be working well now. Thanks for the replies, prompted me to look at it from scratch with fresh eyes which got it working :)
On 1 May 2012, at 10:13 PM, "Modeller Caretaker" modeller-care@salilab.org wrote:
> On 04/26/2012 06:54 AM, Offord, Victoria wrote: >> 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! > > Your alignment file and Python script look fine to me. What happens when you run it? > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
participants (3)
-
Joel Tyndall -
Modeller Caretaker -
Offord, Victoria