November 2003 - modeller_usage

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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MacOS X Modeller 6v2
by Jack Howarth 20 Nov '03

20 Nov '03

Hello, The maintainer of the MacOS X version of Modeller 6.0 may want to consider installing fink 0.6.2 (from fink.sourceforge.net) and 'fink install' the gcc 3.4 g77 compiler to do the next build of Modeller 6.0 under Panther. While the gcc 3.4 g77 compiler isn't as agressive in optimization as the IBM XL Fortran for MacOS X compiler, it does a much better job than before (if used at -O3). This now enables the DFA ppc support in the compiler. I just mention this because the Absoft build of modeller seems a bit sluggish. Unless you have the very latest Absoft MacOSX compilers they might not even generate code as fast as the g77 from gcc 3.4. Otherwise perhaps you need a much higher optimization level setting with the Absoft compiler than you are currently using. Jack Howarth ps If you use g77 3.4 and find that you get compilation error at -O3 you might selectively add -fno-globals to those specific files. The use of -fno-globals on all the source files will impact the performance of the generated code because it disables higher order optimizations. So that should be avoided. ------------------------------------------------------------------------------ Jack W. Howarth, Ph.D. 231 Albert Sabin Way NMR Facility Director Cincinnati, Ohio 45267-0524 Dept. of Molecular Genetics phone: (513) 558-4420 Univ. of Cincinnati College of Medicine fax: (513) 558-8474

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problems with heteroatoms
by Knoll, Michael 19 Nov '03

19 Nov '03

Hi modellers, I have some problems with including heteroatoms in my models. In my pdb-template file there is an HETATM entry at the end (in this case it´s CA). I've switched the HETATM_IO option on in the modeller top-file. Now if I add the residue type number 3 at the end of my alignment, it looks like this : >P1;755 structure:755: : : : : : : : . . . THANRLKLAGV3* >P1;5 sequence:5: : : : : : : : . . . THANRLLLAGV3* This additional entry leads to models which have the correct heteroatom modelled. Now I want to change the residue type number 3 into a wildcard so that in other cases every possible heteroatom could be modelled without looking at the template pdb-file. If I place . instead of 3, the modeller log-file shows following error-massage : Alignment sequence not found in PDB file: Can you tell me if it´s possible to use such a wildcard, or do I have to select the right residue type number for each HETATM-type. Thanks in advance, Michael --

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Modeling Multidomain proteins
by Tjaart de Beer 18 Nov '03

18 Nov '03

Hi there I would like to model a multidomain protein but when I follow the instructions given in the manual I only only get a model based on the first structure in my alignment file. It totally ignores the second structure. There is no overlap between the domains. The top file and alignment file is attached. Can anyone help? Thanks!! -- Tjaart de Beer Bioinformatics and Computational Biology Unit Department Biochemistry FABI 2/BCBU building Faculty of Natural Sciences University of Pretoria Lynwood rd Pretoria South Africa 0001 Tel: +27 12 420 5802 Cell: +27 83 504 7914 Fax: +27 12 420 5800 Email: tjaart(a)tuks.co.za tjaartdb(a)absamail.co.za >P1;pf sequence:pf:1:A:611::::: METIQELILSEENKTNIAVLNLGTNDRRNAVLILETALHLVEKYLGKIINTSYLYETVPEYIVLDKK FYNLTVVVKTFVNDPLSMLVVIKYIE-ELMKRENVKEKEKFENRIIDIDILFFNDFTIFMKNIKLEKNMIYKILSKYIHLERDIKNGNDNMSKVNMDKDINLNNNNNIKKKNNNDIDCDCVDQKMNNHVNNKNYINSFRDPQEIINNMVD NIEFLSIPHVYTTHRYSILLCLNDMIPEYKHNVLNNTIRCLYNKYVSRMKEQYNINIKENNKRIYVLKDRISYLKEKTNIVGILNV-----------NYDSFSDGGIFVEPKRAVQRMFEMINEGASVIDIGGESSAPFVIPNPKISERDLVVPVL QLFQKEWNDIKNKIVKCDAKPIISIDTINYNVFKECVDNDLVDILNDISACTNNPEIIKLLKKKNKFYSVVLMHKRGNPHTMDKLTN-YDNLVYDIKNYLEQRLNFLVLNGIPRYRILFDIGLGFAKKHDQSIKLLQNIHVYDEY-----PLFIGY SRKRFIAHCMNDQNVVINTQQKLHDEQQNENKNIVDKSH-NWMFQMNYMRKDKDQLLYQKNICGGLAIASYSYYKKVDLIRVHDVLETKSVLDVLTKIDQV-* >P1;1DY3 structureX:1DY3:1:A: 158:A:::: ---------------TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPD YLNAAVALET-SLAPEELLNHTQRIE-LQQGRVRK--AERWGPRTLDLDIMLFGNEVINTER-----LTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW----------------------------------- ------------------------------------------------------------------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------------* >P1;1eye structureX:1eye:5:A:274:A:::: ------------------------------------------------------------------- ------------------------------------------------------------------------------------------------------------------------------------------------------ ----------------------------------------------------------------------------PVQVMGVLNVTDDSFSDGGCY-----------LDLDDAVKHGLAMAAAGAGIVDVGG--------------ETSRVIPVV KELAAQG-------------ITVSIDTMRADVARAALQN-GAQMVNDVSGGRADPAMGPLLAEA--DVPWVLMHWRAVSADTPHVPVRYGNVVAEVRADLLASVADAVAAGVDPARLVLDPGLGFAKT-AQHN--WAILHALPELVATGIPVLVGA SRKRFLGALLAGPD-GVMRPTDGRD-TATAVISALAALHGAWGV------------------------------------RVHDVRASVDAIKVVEAWMGAE* INCLUDE # Include the predefined TOP routines SET PDB_EXT = '.pdb' SET ALNFILE = 'HPPK-DHPS1.ali' # alignment filename SET KNOWNS = '1eye' # codes of the templates SET KNOWNS = '1DY3' SET SEQUENCE = 'pf' # code of the target #SET HETATM_IO ='on' #SET WATER_IO = 'on' #SET TOPOLOGY_LIBRARY = $(LIB)/top_heavy.lib #SET PARAMETERS_LIBRARY = $(LIB)/par.lib SET ATOM_FILES_DIRECTORY ='/hosts/milliways/people/tjaart/home/My_Documents/Bifunctional_modelling/' # directories for input atom files SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 SET OUTPUT_CONTROL = 1 1 1 1 1 #SET FINAL_MALIGN3D = 1 CALL ROUTINE = 'model' # do homology modelling SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = 'on' MAKE_RESTRAINTS RESTRAINT_TYPE = 'alpha', RESIDUE_IDS = '594' '607' END_SUBROUTINE

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Question (HELP !!)
by Shunsaku Takeishi 18 Nov '03

18 Nov '03

Dear Dr. Sameer Hassan I would like to ask additional questions. The question is about Error mess age during Modeller performing. The error message is as below ##########ERROR MESSAGES.########## pair2___223E> Array too small. Increase MPAIRS current maximum, current need: 20454 20454 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 16848845 16 453.950 16.068 ##########ERROR MESSAGES.########## Could you please let me know the meaning of the error message and the way o f this trouble shooting. I am very glad if you kindly and immediately treat this matter. Thank you and regards, Shunsaku Takeishi Osaka University xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx 武石俊作（Shunsaku Takeishi）大阪大学大学院理学研究科生物科学専攻　生物物質学大講座　生体分子機能学グループ (倉光研究室) shunt(a)bio.sci.osaka-u.ac.jp xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

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modeling a dimer
by Rao, Guru 14 Nov '03

14 Nov '03

Hi: I am working with a protein which we have characterized to be a dimer. Homologous proteins are also dimers and the 3D structures are of the dimeric forms. In these proteins, the amino acid sequence of the dimer is represented as A and B chains. Can I model my protein as a dimer by arranging my sequence as A and B chains with a " | " in between? Would appreciate some thoughts. Thanks, Guru Rao This communication is for use by the intended recipient and contains information that may be privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html

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fix ligand atom positions during modelling
by Peter Haebel 14 Nov '03

14 Nov '03

Hi there, i would like to build a homology model of a protein-ligand complex. how can I fix the position of my ligand? kind regards, peter -- ___________________________________________ Dr. Peter Haebel Philipps-Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6 D-35032 Marburg phone: +49-6421-28-25072 fax: +49-6421-28-28994 email: peter.haebel(a)staff.uni-marburg.de http://www.agklebe.de

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Respected Sir.
by sameer hassan 10 Nov '03

10 Nov '03

Respected Sir, I am interested in knowing more about modeller. So, I request you to help me for the same. The following are the questions: 1) what is the protocol for starting with the top scripts, i.e, starting with alignment that what..? 2)is transfer_xyz.top to be carried out first before model-default or the other way? 3) will not modeller(model-default.top) itself build the loop. Then why is the loop top script for? if i want to bulit the loop separately using loop top script, is it that i have to carry out loop topscript first before model-default top script or the other way? 4)During model-default. top, if for certain residues co-ordinates are not assigned then what is the solution for that? 5)In one of the article, i have read, after building the model it is to compare the Z score for both the template and the target. where will be the Z score given, will it be given in the log file of model-default. 6)will modeller show any error if the target and the template sequences differ in lenght? 7)After building a model for the target, how will i be able to improve the structure? if i iterate the same procedure will it improve the structure? I would be grateful to you if you could help me in finding answers for the above questions. Thanking you and waiting for your reply. Sincerely, Sameer. H

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Installation on MacOSXvx
by bose 06 Nov '03

06 Nov '03

Hi, I have tried to install Modeller6v2 on the MacOSXv2 and it seems like the installation works but then the mod6v2 command is not recognized. My .cshrc file has been modified and contains all the settings that is suggested in the ReadMe file. Could I have some advice on how to get the program kicking. Thank you. Regards, Bose.

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How many swap space does MODELLER need??
by B.Liu 06 Nov '03

06 Nov '03

A silly problem, but it is a problem. Thanks for any advice. Binbin

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