May 2009 - modeller_usage

(no subject)
by subarna thakur 29 May '09

29 May '09

Hi I am using the model-ligand.py script. My protein in multi-chained, do I have to make changes in the header of the aligenment file? I have put (.) sign at the end of the alignment file and also made option env.io.hetatm is set to True but when I am running the model-ligand.py, a error is coming that there is a mismatch between the alignment and PDB. Subarna Thakur Explore and discover exciting holidays and getaways with Yahoo! India Travel http://in.travel.yahoo.com/

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how add FE-S cluster in PDB
by subarna thakur 29 May '09

29 May '09

Dear User My template has a ligand of Fe-S cluster but when I am generating my PDB file based on this template, it is without any metal ligand..I want to know how do I incorporate the metal cluster in correct position in my PDB file. Subarna thakur Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com

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Re: [modeller_usage] loop refining of a multi chain protein
by subarna thakur 29 May '09

29 May '09

Dear Sir Thanks for suggestion ,it worked. After running the script two PDB files are generated one with extension .BL00010001 and other with .IL00000001 extension.Which one should I select and on which basis? ________________________________ From: Dinesh Babu KR <kr.dineshbabu(a)gmail.com> To: subarna thakur <thakur.subarna(a)yahoo.co.in> Sent: Friday, 29 May, 2009 11:51:19 AM Subject: Re: [modeller_usage] loop refining of a multi chain protein hi in the loop script file you have to mention the chain like this self.residue_range('77:B', '80:B') regards, dinesh On Fri, May 29, 2009 at 1:49 PM, subarna thakur <thakur.subarna(a)yahoo.co.in> wrote: Dear User I have a protein with multichain and I am using loop.py script for refining a protein but a error is coming which suggests that it fails to indentify the metioned residues in pdb file. But when I am running the same loop.py script with a alignment file and PDB file without mentioning any chain, it seems to run ok.. In case of multichain proteins what should be the changes made to the loop.py script for loop refining and how the residues should be mentioned in the script. Subarna thakur ________________________________ Explore and discover exciting holidays and getaways with Yahoo! India Travel Click here! _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org https://salilab.org/mailman/listinfo/modeller_usage Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com

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loop refining of a multi chain protein
by subarna thakur 28 May '09

28 May '09

Dear User I have a protein with multichain and I am using loop.py script for refining a protein but a error is coming which suggests that it fails to indentify the metioned residues in pdb file. But when I am running the same loop.py script with a alignment file and PDB file without mentioning any chain, it seems to run ok. In case of multichain proteins what should be the changes made to the loop.py script for loop refining and how the residues should be mentioned in the script. Subarna thakur Share files, take polls, and make new friends - all under one roof. Go to http://in.promos.yahoo.com/groups/

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Fully automated alignment and modeling
by mzugravu＠buffalo.edu 27 May '09

27 May '09

Hello everyone! I'm trying to do fully automated alignment and modeling on a target sequence having a template sequence. Could you please tell me where I can create .py (python) files and .erg files like the ones used in the online tutorial page Fully automated alignment and modeling? Thank you very much.

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(no subject)
by Ha Hung Chuong Nguyen 27 May '09

27 May '09

Hi mzugravu, I guess there are at least some. In my case, when I have the alignment, I often using Jalview to open it and export to PIR format. Bests, Chuong mzugravu(a)buffalo.edu wrote: > Hello! > Could you please tell me which program should I use to write an alignment file in the PIR format? > Thank you. > > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > https://salilab.org/mailman/listinfo/modeller_usage ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/

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alignment file in the PIR format
by mzugravu＠buffalo.edu 27 May '09

27 May '09

Hello! Could you please tell me which program should I use to write an alignment file in the PIR format? Thank you.

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helix model
by Jairo Rocha 20 May '09

20 May '09

Hi all. I have some sequences from real bacteria that correspond to one protein in the pdb, 1SIG. Of course, they have lots of mutations. I would like to know which changes the structure would have, due to these mutations. I used Modeller to answer that question, for the first time. The predicted structures are very very similar to the given structure. I am surprised that some helices are not broken or bended just a bit. So I did the following experiment: I replaced in the sequence, by hand, twenty amino acids that correspond to a helix in 1SIG, with 20 amino acids that are already in a loop in the sequence. Then I asked Modeller to calculate the structure and I get almost the same structure again, with helix, even in the part in which I replaced the helix sites. As far as I know, to get a helix requires several energy states to coincide, so it is difficult that by change I get the helix. So it seems to me the program just copies the structure. The details are the following: 1SIG is from the pdb. I attach the sequence I would like to model, Ppertucin, and the alignment between them. I also attach the hand modified sequence, Ppertucintest in which the 23 amino acids DPDDDGLSGTDNAVVPAAAAKPKD (that are present in Ppertucin (46-69) already but have no alignment with 1SIG) replace 23 amino acids that were between positions 97 and 120, matched to a helix in 1SIG, and I keep the same alignment. The model for Ppertucin does not predicts a helix for the 23 amino acids that correspond to a gap in 1SIG. But when the same 23 amino acids appear again in Ppertucintest aligned to a helix, then the model for Ppertucintest is a helix in that fragment. I can conclude that if I assume the helix is conserved, then it will be, otherwise, not. How can make the results useful? Modeller was not intended for these kind of situations? Thanks for any hint, Jairo Rocha University of the Balearic Islands Spain >Ppertucin RIEEGIREVMAAISMFPGTVDGILTEYQRIAEEGGRLTDIFNGYIDPDDDGLSGTDNAVV PAAAAKPKDEKKASDDDEEEEEDTEDDTEEETDGGPDPEIARQRFGAVQEQLEKVRKVLK AKKGDRSHPDVVAEMETLAQLFMPIKLVPKQYDALVARVRGVQDDIRARERAIMQLCVRD ARMPRADFLRSFPGNETNEKWIDEVLAKKPAYADALAALQPDILRQQQQLIALEQDAQLT IAQV >P1;1SIG.pdb structureX:1SIG.pdb:113:A:446:A:ferredoxin:Peptococcus aerogenes: 2.00:-1.00 MEGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVD----- ------------DLAPTATHVGSELSQE-------------DLDIDPELAREKFAELRAQ YVVTRDTIKA------HATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQER LIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQ QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ* >P1;Ppertucin sequence:Ppertucin:1 :A:244 :A:ferredoxin:Peptococcus aerogenes: 2.00:-1.00 ---------RIEEGIREVMAAISMFPGTVDGILTEYQRIAEEGGRLTDIFNGYIDPDDDG LSGTDNAVVPAAAAKPKDEKKASDDDEEEEEDTEDDTEEETDGGPDPEIARQRFGAVQEQ LEKVRKVLKAKKGDRSHPDVVAEMETLAQLFMPIKLVPKQYDALVARVRGVQDDIRARER AIMQLCVRDARMPRADFLRSFPGNETNEKWIDEVLAKKPAYADALAALQPDILRQQQQLI ALEQDAQLTIAQV----------------------------------------------- -----------------------------------------* >Ppertucintest RIEEGIREVMAAISMFPGTVDGILTEYQRIAEEGGRLTDIFNGYIDPDDDGLSGTDNAVV PAAAAKPKDEKKASDDDEEEEEDTEDDTEEETDGGPDPDDDGLSGTDNAVVPAAAAKPKD AKKGDRSHPDVVAEMETLAQLFMPIKLVPKQYDALVARVRGVQDDIRARERAIMQLCVRD ARMPRADFLRSFPGNETNEKWIDEVLAKKPAYADALAALQPDILRQQQQLIALEQDAQLT IAQV >P1;1SIG.pdb structureX:1SIG.pdb:113:A:446:A:xxx:xxx: 2.00:-1.00 MEGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYNRVEAEEARLSDLITGFVD----- ------------DLAPTATHVGSELSQE-------------DLDIDPELAREKFAELRAQ YVVTRDTIKA------HATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQER LIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQ QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ* >P1;Ppertucintest sequence:Ppertucintest:1 :A:244 :A:xxxx:xxx: 2.00:-1.00 ---------RIEEGIREVMAAISMFPGTVDGILTEYQRIAEEGGRLTDIFNGYIDPDDDG LSGTDNAVVPAAAAKPKDEKKASDDDEEEEEDTEDDTEEETDGGPDPDDDGLSGTDNAVV PAAAAKPKDAKKGDRSHPDVVAEMETLAQLFMPIKLVPKQYDALVARVRGVQDDIRARER AIMQLCVRDARMPRADFLRSFPGNETNEKWIDEVLAKKPAYADALAALQPDILRQQQQLI ALEQDAQLTIAQV----------------------------------------------- -----------------------------------------*

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(no subject)
by David Hall 20 May '09

20 May '09

I'm trying run align2d on 3dxn chain a's pdb and it's sequence provided by the pdb. My code is as below: from modeller import * env = environ() aln = alignment(env) mdl = model(env, file="3dxn_nmin") aln.append_model(mdl, align_codes='structure', atom_files="3dxn_nmin.pdb") aln_block = len(aln) aln.append('3dxn.a.fasta', alignment_format='FASTA') aln.align2d(align_block=aln_block, output_weights_file='2dalign.mtx') aln.check_sequence_structure() aln.write(file='tmp.ali', alignment_format='PIR') In the alignment, I get: >P1;structure structureX:3dxn_nmin.pdb: 19 :A:+258 :A:::-1.00:-1.00 ------------------LSDRYQRVKKLG--SYGEVLLCKDK-TGAERAIKIIKKSSVTTTSNSGALLDEVAVL KQLDHPNIMKLYEFFEDKRNYYLVMEVYRGGELFDEIILRQKFSEVDAAVIMKQVLSGTTYLHKHNIVHRDLKPE NLLLESKS-DALIKIVDFGLSAHFE-------RLGTAYYIAPEVLRKKYDEKCDVWSCGVILYILLCGYPPFGGQ TDQEILKRVEKGKFSFDPPDWTQVSDEAKQLVKLMLTYEPSKRISAEEALNHPWIVKFCSQK* >P1;3DXN:A:sequence sequence:: : : : :::-1.00:-1.00 MHHHHHHSSGRENLYFQGLSDRYQRVKKLGSGAYGEVLLCKDKLTGAERAIKIIKKSSVTTTSNSGALLDEVAVL KQLDHPNIMKLYEFFEDKRNYYLVMEVYRGGELFDEIILRQKFSEVDAAVIMKQVLSGTTYLHKHNIVHRDLKPE NLLLESKSRDALIKIVDFGLSAHFEVGGKMKERLGTAYYIAPEVLRKKYDEKCDVWSCGVILYILLCGYPPFGGQ TDQEILKRVEKGKFSFDPPDWTQVSDEAKQLVKLMLTYEPSKRISAEEALNHPWIVKFCSQK* If you look at the biggest gap, preceded by "HFE" in the alignment, that E should be at the other end of the gap. Sequence-wise, having it at either end is equivalent (there is an E in both places), but the actual pdb file has "ERL" at the other end and "HF" preceding. When I run the check_sequence_structure(), it agrees, saying: Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms: ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------- 174 1 174 182 F E 12.004 END OF TABLE I've placed the files at github if they are of any help They can be cloned at: git clone git://gist.github.com/114942.git Thanks, David

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Tetramer symmetry for hERG
by Du-Cuny,Lei 18 May '09

18 May '09

Dear Sir, I am trying to build a tetramer model for hERG based on the crystal structure KcsA (1BL8.pdb). The modeller did give me four chains, but not the correct symmetry. Since I am new to Modeller, I am wondering whether there is somebody can help me. Thank you, Lei Du-Cuny ------------------------------------------ The following are the alignment file and python script I have used. hERG-KcsA-multialign.ali >P1;1BL8 structureX:1BL8:62: A:111: A:KcsA: : : YPRALWWSVETATTVGYGDLYPVTLWGRCVAVVVMVAGITSFGLVTAALA* >P1;hERG sequence:hERG: : : : :hERG:human: : VT-ALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNV-/ VT-ALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNV-/ VT-ALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNV-/ VT-ALYFTFSSLTSVGFGNVSPNTNSEKIFSICVMLIGSLMYASIFGNV-* model-multichain.py # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A, B, C and D chains to be identical s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, 1)) self.restraints.symmetry.append(symmetry(s2, s3, 1)) self.restraints.symmetry.append(symmetry(s3, s4, 1)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1) env = environ() # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'hERG-KcsA-multialign.ali' , # alignment filename knowns = '1BL8', # codes of the templates sequence = 'hERG') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 10 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling

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