- modeller_usage - salilab.org

modeling different conformations of a protein from related structures
by EGY 07 May '12

07 May '12

I searched the archives and could not find how to do what seems to be a simple procedure. I have a sequence that has high homology with a published X-ray structure A. A second state of the protein is defined by the conformation of a conserved loop. A related protein B containing the conserved loop is in the second state, albeit with lower homology. I would like to model the sequence in the second state using the structure A as a template, but using structure B to model the loop only. I believe I need an alignment like this: proteinA aaaaaaaaaaaaaaaa-------------------aaaaaaaaaaaa proteinB ----------------------------bbbbbbbbbbb--------------------- sequence cccccccccccccccccccccccccccccccccccccccccccccc I realize this is a very simple question. I've been going through the manual and searching the archives and cannot figure out how to do it. Any help will be much appreciated. Thanks. EGY

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Question about alignment.check()
by M 05 May '12

05 May '12

Hello, I have a question about the alignment.check() command (more precisely check_structure_structure). After using this command I get a log which contains many large distances between equivalent pairs of templates. For example, one line of the log looks like this: ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- 21 1 2 39 43 I G 14.905 Using the superimposed templates and a visualisation program (pymol), the measured distance between the mentioned pairs is only 0,6 A. The problem is the same for other pairs. I've checked the alignment pir file many times and there are no errors in it, the sequences are aligned correctly. How can this be explained? Best regards, Mat

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missing residues
by Mary Varughese 04 May '12

04 May '12

hi, I have a dimer protein with missing residues in both subunits. I have the target sequence, the original protein pdb with missing gaps * (a.pdb* resolution 3.58 Xray structure)and another pdb of the same protein with missing residues included (*b.pdb* resolution 3.5 electron diffraction) So i have to add missing residues with b.pdb as the template and rest of the protein exact to a.pdb) In the given example: >P1;1qg8structureX:1qg8: 2 :A: 256 :A:undefined:undefined:-1.00:-1.00PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------------EFVRNLPPQRNCRELRESLKKLGMG*>P1;1qg8_fillsequence:::::::::PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLFELEKNEFVRNLPPQRNCRELRESLKKLGMG* Here what extra alignment should be added if i have a pdb(*b.pdb*) with missing residues included which can be used as a template(same sequence). Also can i add missing residues in both A and B units simultaneously. Thanking you -- Mary Varughese Research Scholar School of Pure and Applied Physics Mahatma Gandhi University India

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Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 54
by Ashish Runthala 04 May '12

04 May '12

No, Mary Varughese. Sir just meant that you should parse your sequence mentioned as M in his alignment (with / being the chain delimiter), (M: your target Model residues and not Missing residue) He simply pointed that You can easily cover up the missing residues of each of chain A and B, through its corresponding coordinate information available in the other chain. So missing residues of A chain you are filling up the gap with B chain, and same way for the other chain. You should not edit the template files and rather use them as such for target sequence as per the manually curated alignment file as Sir has shown. Ashish Runthala, Lecturer, Structural Biology Cell, Biological Sciences Group, BITS, Pilani Rajasthan, INDIA ----- Original Message ----- From: "modeller usage-request" <modeller_usage-request(a)salilab.org> To: "modeller usage" <modeller_usage(a)salilab.org> Sent: Friday, May 4, 2012 12:52:17 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi Subject: modeller_usage Digest, Vol 11, Issue 54 Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit https://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. Re: missing residues (Modeller Caretaker) 2. Re: missing residues (Mary Varughese) ---------------------------------------------------------------------- Message: 1 Date: Thu, 03 May 2012 12:37:34 -0700 From: Modeller Caretaker <modeller-care(a)salilab.org> To: Mary Varughese <maryvj1985(a)gmail.com> Cc: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] missing residues Message-ID: <4FA2DE7E.5060103(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 5/3/12 3:29 AM, Mary Varughese wrote: > I have a dimer protein with missing residues in both subunits. > > I have the target sequence, the original protein pdb with missing gaps > *(a.pdb* resolution 3.58 Xray structure)and another pdb of the same > protein with missing residues included (*b.pdb* resolution 3.5 electron > diffraction) > > So i have to add missing residues with b.pdb as the template and rest of > the protein exact to a.pdb) Yes, that should be fairly straightforward - simply use both templates in modeling, and align the model with a.pdb or b.pdb accordingly. If possible, try to overlap the regions a little so that Modeller can figure out the conformation of the missing regions. > Also can i add missing residues in both A and B units simultaneously. Sure, that's no problem. Your alignment might look something like: >P1;a ... AAAAAAAAAA------AAAAAAAAAA/AAAAAAAAAA------AAAAAAAAAA* >P1;b ... --------BBBBBBBBBB--------/--------BBBBBBBBBB--------* >P1;model ... MMMMMMMMMMMMMMMMMMMMMMMMMM/MMMMMMMMMMMMMMMMMMMMMMMMMM* (This assumes that you've edited b.pdb to only include the regions in the alignment above.) Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ Message: 2 Date: Fri, 4 May 2012 12:52:13 +0530 From: Mary Varughese <maryvj1985(a)gmail.com> To: modeller_usage(a)salilab.org Subject: Re: [modeller_usage] missing residues Message-ID: <CAAjRZU0+Ht-HtyqDNn64g-p_5Z5r_Y1QDG3_dqaX+Xn1jhe0xA(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Sir, Did you mean that i should edit the template(for missing residues) pdb so that it contains the co-ordinates of the missing residues only. ; and the alignment look likes ---------------------mmmmmmmm-------------------* where m stands for missing residues.? But what you mean by overlap the regions a little so that modeller can figure out the conformation of the missing regions? Thank you very much for your reply On Thu, May 3, 2012 at 3:59 PM, Mary Varughese <maryvj1985(a)gmail.com> wrote: > hi, > > I have a dimer protein with missing residues in both subunits. > > I have the target sequence, the original protein pdb with missing gaps * > (a.pdb* resolution 3.58 Xray structure)and another pdb of the same > protein with missing residues included (*b.pdb* resolution 3.5 electron > diffraction) > > So i have to add missing residues with b.pdb as the template and rest of > the protein exact to a.pdb) > > In the given example: > > > >P1;1qg8structureX:1qg8: 2 :A: 256 :A:undefined:undefined:-1.00:-1.00PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLN---DIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYIT--------------EFVRNLPPQRNCRELRESLKKLGMG*>P1;1qg8_fillsequence:::::::::PKVSVIMTSYNKSDYVAKSISSILSQTFSDFELFIMDDNSNEETLNVIRPFLNDNRVRFYQSDISGVKERTEKTRYAALINQAIEMAEGEYITYATDDNIYMPDRLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQVTWNAPCAIDHCSVMHRYSVLEKVKEKFGSYWDESPAFYRIGDARFFWRVNHFYPFYPLDEELDLNYITDQSIHFQLFELEKNEFVRNLPPQRNCRELRESLKKLGMG* > > Here what extra alignment should be added if i have a pdb(*b.pdb*) with > missing residues included which can be used as a template(same sequence). > > Also can i add missing residues in both A and B units simultaneously. > > Thanking you > -- > Mary Varughese > Research Scholar > School of Pure and Applied Physics > Mahatma Gandhi University > India > > -- Mary Varughese Research Scholar School of Pure and Applied Physics Mahatma Gandhi University India

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2 BLK in one model
by Isaure Chauvot de Beauchêne 01 May '12

01 May '12

Hi, I'm trying to model a complex of 3 components: a peptide including 2 phosphotyrosines, and 2 signal protein recognizing each one phosphotyrosine. I have 2 templates, one for each complex protein-phosphopeptide. I've put each PTR as BLK. But one of the PTR is changed in ASP in my results, because Modeller change the alignment I gave in my .ali file. This is the alignment file: > P1;2iuh #Pi3k structureX:2iuh:4:A:208:B:::: -------------------------------------------------------------------------------- --------------------------NMSLQNAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNN KLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKE-/ TNE.MDMK-------------* > P1;2pld #PLC structureX:2pld:1:A:12:B:::: GSPGIHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDL ISYYEKHPLYRKMKLRYPINEENSS/------------------------------------------------------- --------------------------------------------------------------/ ---------DNDYIIPLPDPK* > P1;comp sequence:comp:1:A:21:C:::: GSPGIHESKEWYHASLTRAQAEHMLMRVPRDGAFLVRKRNEPNSYAISFRAEGKIKHCRVQQEGQTVMLGNSEFDSLVDL ISYYEKHPLYRKMKLRYPINEENSS/NMSLQNAEWYWGDISREEVNEKLRDTADGTFLVRDASTKMHGDYTLTLRKGGNN KLIKIFHRDGKYGFSDPLTFSSVVELINHYRNESLAQYNPKLDVKLLYPVSKYQQDQVVKED/ TNE.MDMKPGVSYVVPTKADK* and this is part of the .out: read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 120) Alignment ETNE.MDMK PDB ETNEMDMK Match ***** Alignment residue type 11 (M, MET) does not match pdb residue type 3 (D, ASP), for align code 2iuh (atom file 2iuh), pdb residue number "206", chain "B" This is the PTR of the template 2iuh: ATOM 967 CD GLU B 203 28.500 18.086 19.085 1.00 23.93 C ATOM 968 OE1 GLU B 203 28.474 16.841 18.975 1.00 25.60 O ATOM 969 OE2 GLU B 203 29.534 18.753 18.901 1.00 25.56 O1- HETATM 970 N BLK B 204 23.987 20.311 19.503 1.00 17.56 N HETATM 971 CA BLK B 204 23.170 20.645 18.345 1.00 17.48 C HETATM 972 C BLK B 204 23.958 20.440 17.054 1.00 17.87 C HETATM 973 O BLK B 204 25.071 20.949 16.905 1.00 17.97 O HETATM 974 CB BLK B 204 22.668 22.083 18.435 1.00 16.51 C HETATM 975 CG BLK B 204 21.236 22.165 18.925 1.00 16.28 C HETATM 976 CD1 BLK B 204 20.236 21.731 18.070 1.00 16.08 C HETATM 977 CD2 BLK B 204 20.937 22.626 20.204 1.00 15.99 C HETATM 978 CE1 BLK B 204 18.914 21.746 18.468 1.00 15.70 C HETATM 979 CE2 BLK B 204 19.616 22.637 20.615 1.00 15.90 C HETATM 980 CZ BLK B 204 18.643 22.197 19.729 1.00 16.36 C HETATM 981 OH BLK B 204 17.254 22.157 20.018 1.00 16.93 O HETATM 982 P BLK B 204 16.513 22.838 21.260 1.00 16.40 P HETATM 983 O1P BLK B 204 15.064 22.662 21.118 1.00 15.57 O HETATM 984 O2P BLK B 204 16.982 22.261 22.527 1.00 16.50 O1- HETATM 985 O3P BLK B 204 16.829 24.260 21.166 1.00 17.35 O ATOM 986 N MET B 205 23.429 19.583 16.187 1.00 17.64 N ATOM 987 CA MET B 205 24.111 19.203 14.953 1.00 17.33 C ATOM 988 C MET B 205 23.824 20.152 13.795 1.00 17.59 Do you have an idea of why Modeller switch the PTR of my template? Many thanks in advance, Isaure -- Isaure Chauvot de Beauchêne Ph.D student Team: "Bioinformatics, Modelisation and Molecular Dynamics" (BiMoDyM) Dir Luba Tchertanov,LBPA-CNRS, ENS-Cachan 61 Av du Pr Wilson, 94230 Cachan, FRANCE

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modelling with hetatms
by Offord, Victoria 01 May '12

01 May '12

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....*

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Loop refinement: setting the right anchors in multichain models
by Jérôme Hénin 01 May '12

01 May '12

Hi everyone, I am trying to do loop refinement on a multi-chain protein. My problem is that Modeller tries to anchor C-ter loops to the N-ter of the next chain, yielding unrealistic starting configurations, and making the whole refinement fail. How can I instruct Modeller that the C-ter and the following N-ter "loops" are to be modeled separately? Thanks, Jerome

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procheck problem.
by vishal Nemaysh 30 Apr '12

30 Apr '12

Respected Sir, I have tried to minimize my pdb structure which is modeled by Modeller9v8. i use the Discovery Studio plateform to minimize this pdb structure by applying CHARMm force field and applying steepest descent and after that conjugate gradient algorithm. but the problem here is that the procheck result is not good as earlier. such as in Ramachandran plot 87% amino acids are in favorable region before minimization but after minimization only 55% amino acids are in favorable range...so plz sir suggest me some solutions.... Thanking you, Your Sincerely -- Vishal Research Scholar, University of Delhi, North Campus Delhi-110007 M: 91+9650736653

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Re: [modeller_usage] (no subject)
by sree jyothi 27 Apr '12

27 Apr '12

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Invitation to connect on LinkedIn
by Uday Kumar 26 Apr '12

26 Apr '12

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