modeller_usage June 2003

modeller_usage@salilab.org

16 participants
11 discussions

Modeller input alignment file
by christos Kouriniadis 26 Jan '04

26 Jan '04

Hello everybody, I am doing a project on comparative modelling, by using modeller. My problem is the following: I am trying to make an input file with PDB structures aligned in PIR format. However, when I am reading the modeller manual, I see that the worked example is in the form: P1;2ald structureX:2ald:2:@:363:@:aldolase:human muscle:2.00:0.17 * If you go to the section "display/download file", in the PDB website, you will get the usual big file. But when I have a look at this file, I see that ATOM has three coordinates: -20.521 45.890 70.464 How from these coordinates I get the :2:@:363:@: ??? Is there a formula that transforms it? I would be grateful if you could give me a hint on this. Thanks, Christos Kouriniadis _________________________________________________________________ Add photos to your e-mail with MSN 8. Get 2 months FREE*. http://join.msn.com/?page=features/featuredemail

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log file
by truename 30 Jun '03

30 Jun '03

I do not know how to obtain a log file with error message with in it. Are there anybody who can help me? YeBin

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B factor column?
by Margot Ernst 30 Jun '03

30 Jun '03

Hello, apologies if this is covered in the documentation, I didn't find it: What is in the B-factor column of the PDB files Modeller writes? Thanks, margot -- ----------------------------------------------------------------- | Dr. Margot Ernst | Abteilung Prof. Sieghart | Institut f. Hirnforschung/brainresearch institute | Spitalgasse 4 | A-1090 WIEN VIENNA, Austria | margot.ernst(a)univie.ac.at | visit http://www.univie.ac.at/brainresearch ----------------------------------------------------------------- the bottom line to brainresearch: If the brain was so simple that you could understand it, you would be so simple that you couldn't. (unknown) --------------------------------------------------------- "Research: If it worked the first time, they would just call it 'search'." -Roy Garcia -------------------------------------------------------- -----------------------------------------------------------------

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FW: top file problem
by Modeller Care 28 Jun '03

28 Jun '03

Forwarded by list-owner: ------ Forwarded Message From: "truename" <yb_108(a)yeah.net> Date: Sat, 28 Jun 2003 17:48:51 +0800 (CST) To: "modeller care" <modeller-care(a)salilab.org> Subject: Re: your modeller question Dear Ursula Pieper: Thank you for your reply! How ever both the sequence that I used to align and pdb file are from the PDB.They are exactly corrospondent file for the same protein. The content of p.top are as following ___________________________________________________________________________ # Very fast homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET ALNFILE = 'Together2.ali' # alignment filename SET KNOWNS = '1DBG_A' '1AIR_' # codes of the templates SET SEQUENCE = 'T0101' # code of the target SET ATOM_FILES_DIRECTORY = './:../1DBG_A 1AIR_' # directories for input atom files SET STARTING_MODEL = 2 SET ENDING_MODEL = 2 SET OUTPUT_CONTROL = 1 1 1 1 2 # SET OUTPUT = 'LONG' SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'very_fast' # prepare for extremely fast optimization CALL ROUTINE = 'model' # do homology modelling ___________________________________________________________________________ and my p.aln file are as follwing ___________________________________________________________________________ >P1;1DBG_A structureX:1DBG_A:1 : :506 : : : : : ----MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVKEVKPGGLVQIADGTY-- -----KDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRA IQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTD KITFDQVINLNNTARAIKDGSVGGPGMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGR CLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQR FGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFIN VNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKN SWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDE VRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH* >P1;T0101 sequence:T0101:1 : :400 : : : : : ADCSSDLTSGISTKRIYYVAPNGNSSNNGSSFNAPMSFSAAMAAVNPGELILLKPGTYTI PYTQGKGNTITFNKSGKDGAPIYVAAANCGRAVFD----------FSFPDSQWVQAS--- --------------YGFYVTGDYWYFKGVEVTRAGYQGAYVIGSHNTFENTAFHHN---- ----------RNTGLEINNG--GSYNTVINSDAYRNYDPKKNGSMADGFGP-KQKQGPGN RFVGCRAWENSDDGFDLFDS--PQKVVIENSWAFRNGINYWNDSAFAGNGNGFKLGGNQA VGN-------HRITRSVAFGNVSKGFDQNNNAGGVT---------------VINNTSYKN GINYGFGSNVQSGQK----------------------HYFRNNVSLSASVTVSNADAKSN SWDTGPAASASDFVSLDTSL------------------------ATVSRDNDGTLPETSL FRLSANSKLINAGTKESNISYSGSAPDLGAFERN---* >P1;1AIR_ structureX:1AIR_:1 : :353 : : : : : ---------ATDTGGYAATAGGNVTGAVSKTATSMQDIVNIIDAARLDANGKKVKG---- -----GAYPLVITYTGNEDSLINAAAAN--------------------ICGQWSKDPRG- --------------VEIKEFTKGITIIGANGSSANFGIWIKKSSDVVVQNMRIGYLPGG- ----------AKDGDMIRVD--DSPNVWVDHNELFAANHECDGTPDN-----------DT TFESAVDIKGASNTVTVSYN-----YIHGVKKVGLDGSSSSDTGRNITYHHNYYNDVNAR LPLQ-------RGGLVHAYNNLYTNITGSGLNVRQN------------------GQALIE NNWFEKAINPVTSRY--------------------------DGKNFGTWVLKGNNITKPA DFSTYSITWTADTKPYVNAD---------------------------SWTSTGTFPTVAY N----YSPVSAQCVKDKLPGYAGVGKNLATLTSTACK* ___________________________________________________________________________ Best Regards YeBin Error message: > However, some difficulties confronted me during my first project of > protein modelling. Do you lend me a hand to solve it? > The error messages are as following: > ________________________________________________ > rdpir____648E>Alignment sequence not found in PDB file: 1 ./1AIR.atm > recover_____E>ERROR_STATUS >=STOP_ON_ERROR: 1 1 > > And p.top and p.ali are included in the attachment > > Thanks a lot! > Best regards > > YeBin > > > ------ End of Forwarded Message >

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How to include the modified residues in the alignment (.pir file)
by mxue＠rdg.boehringer-ingelheim.com 16 Jun '03

16 Jun '03

Hello, Does anybody know if I can include the modified residue such PTR for Y in the .pir file? Or how can I tell Modeler to read the HETATM PTR as a Y? Thanks. Ming

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Re: Modeller input alignment file
by Modeller Care 16 Jun '03

16 Jun '03

forwarded for majordomo reasons ---------------------------------------------------- Hello Christos, you will find the information you seek at http://salilab.org/modeller/manual/node83.html#alignmentformat , and an example from the user-list: http://salilab.org/cgi-bin/lwgate/lwgate/MODELLER_USAGE/archives/modelle r_usage.archive.02/Author/article-437.html For short, 2:@:386:@ means: number_first_aminoacid_in_pdb_file:name_of_chain:last_aminoacid:name_of_ chain, so if your structure has the first 10 aminoacids missing, the last aminoacid available is numbered 432, and the chain is named "B" in the pdb-file, then this should be 11:B:432:B . Best wishes, Thorsten Schweikardt Molecular Biophysics University of Mainz ------ End of Forwarded Message

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FW: Modeller6v2 trouble
by Modeller Care 12 Jun '03

12 Jun '03

------ Forwarded Message From: Mario Garcia <sbioi000(a)cib.csic.es> Date: Fri, 21 Mar 2003 16:53:17 +0100 (CET) To: modeller-care(a)salilab.org Subject: Modeller6v2 trouble Dear Dr. Bozidar, I have some error after a modeling jot execution (mod script.top) in Modeller6v2 under an IRIX 6.2 box. Bellow, I include the corresponding .top and .ali input files and the resulting .log file. Could you give some hints to help me? Thank you very much in advance for your help. Regards, Mario Garcia. ------------------------------------------------------------------------- Mario Garcia de Lacoba, PhD. Phone : +341 915611800 (ext.4334) Fax : +341 915627518 Centro de Investigaciones Biologicas E-mail : mario(a)cib.csic.es C.S.I.C. c/ Velazquez, 144 28006-Madrid. SPAIN. ------------------------------------------------------------------------- ======================MOB3.top=================================== # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'MOB4.ali' # alignment filename SET KNOWNS = '1cii' # codes of the templates SET SEQUENCE = '1mob' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CHECK_ALIGNMENT CALL ROUTINE = 'model' # do homology modelling ================MOB4.ali================================ C; mob_1cii.phy align >P1;1cii structureX:1cii EIMAVDIYVNPPRVDVFHGTPPAWSSFGNKTIWGGNEWVDDSPTRSDIEK RDKEITAYKNTLSAQQKENENKRTEAGKRLSAAIAAREKDENTLKTLRAG NADAADITRQEFRLLQAELREYGFRTEIAGYDALRLHTESRMLFADADSL RISPREARSLIEQAEKRQKDAQNADKKAADMLAEYERRKGILDTRLSELE KNGGAALAVLDAQQARLLGQQTRNDRAISEARNKLSSVTESLNTARNALT RAEQQLTQQKNTPDGKTIVSPEKFPGRSSTNDSIVVSGDPRFAGTIKITT SAVIDNRANLNYLLSHSGLDYKRNILNDRNPVVTEDVEGDKKIYNAEVAE WDKLRQRLLDARNKITSAESAVNSARNNLSARTNEQKHANDALNALLKEK ENIRNQLSGINQKIAEEKRKQDELKATKDAINFTTEFLKSVSEKYGAKAE QLAREMAGQAKGKKIRNVE-EALKTYEKYRADINKKINAKDRAAIAAALE SVKLSDISSNLNRFSRGLGYAGKFTSLADWITEFGKAVRTENWRPLFVKT ETIIAGNAATALVALVFSILTGSALGIIGYGLLMAVTGALIDESLVEKAN KFW* >P1;1mob sequence:1mob ------MSYMVARMQKMKAGNLGGAFKHNERVFETHSNKDINPSRSHLN- --YELTDRDRSVSYEKQIKDYVNENKVSNRAIRKDAVLCDEWIITSDKD- -----------FFEKLDEEQTRTFFETAKNYFAENYG-ESNIAYASVHLD ESTPHMHMGVVPFENGKLSSKAMFDREELKHIQEDLPR--YMSDHGFELE -------------------------------RGKLNSEAKHKTVAEFKRA MADMELKEELLEKYHAPLFVDERTG--ELNNDTEAFWHEKEFADMFEVQS PIRETTNQEKMDWLRKQYQEELKKLESSKKP-LEDDLSHLEELLDKKTKE YIKIDSEASERASELSKAEGYINTLEN--HSKSLEAKIECLESDNLQLEK Q----KATKLEAKALNES----ELRELKPKKNFLGKEHYELSPEQ---FE GLKAEVYRSRTLLHHKDIELEQAKRQVSLRASKNYFTASLERAKEKAKGE SIDR--LKSEIKRLKN------------E----N-SILRQQNDK-MLGKL RELMPDKAFKNLLSELKAIKP-----------IVNIIKKAIEKSLF---- ---* =====================MOB4.log================================= MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 akilonia 6.5 IP30 Date and time of compilation : 07/05/2002 17:12:26 Job starting time (YY/MM/DD HH:MM:SS): 2003/03/21 23:47:53.033 TOP_________> 105 705 SET ALNFILE = 'MOB4.ali' TOP_________> 106 706 SET KNOWNS = '1cii' TOP_________> 107 707 SET SEQUENCE = '1mob' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_335E> No alignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2200483 2148.909 2.099 Starting time : 2003/03/21 23:47:53.033 Closing time : 2003/03/21 23:48:02.202 Total CPU time [seconds] : 0.00 ------ End of Forwarded Message

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RE: problem in installing modeller
by Andrej Sali 11 Jun '03

11 Jun '03

Hopefully somebody on modeller_usage(a)salilab.org will respond. a -- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4258 Email sali(a)salilab.org; Web http://salilab.org > -----Original Message----- > From: hjslfad lhasfh [mailto:pannirselvam_m@yahoo.com] > Sent: Tuesday, June 10, 2003 7:15 AM > To: sali(a)salilab.org > Subject: problem in installing modeller > > > respected sir/madam, > > while installing the modeller, i > encountered a peculiar problem. The installation of > files was proper, but when i try to run 'mod6v2' > executable file in modeller's bin directory, i am > getting the error message as "command not found". > > so kindly provide me with further > information to install the program > > yours sincerely > > pannir > > __________________________________ > Do you Yahoo!? > Yahoo! Calendar - Free online calendar with sync to > Outlook(TM). http://calendar.yahoo.com >

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MULTIPLE/SINGLE templates for modelling.
by Mr.Sridhar 10 Jun '03

10 Jun '03

I have two basic questions which I am desperate to get answers. Any body there who can help me ? ----------------------------------------------------------------------- 1. In homology based modelling is it good to use single template or multiple templates? I have a cytochromep450 protein which shares maximum homology with another protein of same class . But there were some missing residues in the template. When used for modelling the region corresponding to this missing region had bad environments in Verigy3D. I went on for loop modelling for this region. But is this a good approach ? I feel the alignment itself should take care of everything. I heard about using multiple templates in such cases. How is this approach followed and how good is it ? -------------------------------------------------------------------------- 2. I need to model some point mutations into this same protein sequence. What is the best way of introducing mutations. Should the mutations be introduced in the sequence and then modelled seperately, or should they be introduced in the model of the wildtype ? I want to do molecular dynamic simulations on Wildtype and Mutants to compare and contrast the wildtype and mutant structures. What effect would both these approaches have on the correctness of my results. ---------------------------------------------------------------------------- I'll be very grateful to you for your patience for all your suggessions for my quieries. Thanking you, sridhar

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Re: FW: model a protein
by Eric Feyfant 02 Jun '03

02 Jun '03

You should check the Align2D command Eric ------------------------------------ Eric Feyfant, Ph.D. Computational Chemistry Wyeth Research 200 Cambridge Park Drive Cambridge, MA 02140 tel: +1 617 665 5656 fax: +1 617 665 5682 email: efeyfant(a)wyeth.com >>> Modeller Care <modeller-care(a)salilab.org> 06/02/03 12:18PM >>> Forwarded by the list owner ----------------------------------------------------- Dear Sir, I have a few questions before starting modelling. I would like to know how one can use modeller for aligning the sequences that have the structure (treated as templates for modelling) and that do not have a solved structure (our target). I couldn't get the answer for this question from the modeller tutorial. Expecting the answer as soon as possible. Thanking You Nethaji

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modeller_usage June 2003