- modeller_usage - salilab.org

problem in installing
by rathankar rao 02 Dec '03

02 Dec '03

hi i have installed modeller6v2 in c:/ in windows68se OS, i also recieved my license key from the author but on entering the license key to modenv.bat and mod.bat, it says wrong license the license provided to me is ****. i dont know how to go with it plz advice N.Rathankar Assistant Proffessor in physics Madanapalle Institute of Technological Sciences (MITS). INDIA WEBSITE: http://www.geocities.com/rathankar/ --------------------------------- Do you Yahoo!? Free Pop-Up Blocker - Get it now

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Re: [modeller_usage] malign3d will not align multiple structures
by Mark Daniels 01 Dec '03

01 Dec '03

Hello Oliver- Thank you for the reply. MALIGN3D does not require an alignment file if the structural models have a 1:1 sequence correspondence. In my case I am aligning five models of the same protein. I figured out what the problem was by looking at the .top files in the examples/tutorial-model folder of modeller6v2. As it turns out, I have to add the command SET ALIGN_CODES = 'atip' 'atip' 'atip' 'atip' 'atip' with which MALIGN3D properly loads the five model atip.Bxxx files. The Sanchez and Sali Methods in Molecular Biology article does not mention this (and neither does the manual). Regards- Mark J Daniels markjd(a)scripps.edu Department of Cell Biology The Scripps Research Institute La Jolla, CA On Mon, 1 Dec 2003, Oliver Hucke wrote: > Hi Mark, > > I miss the specification of the alignment file in your top script. I > suppose modeller needs an initial alignment - at least that's how I use > MALIGN3D. The atom files are specified in the alignment file, not in the > script. Please have a look at the example given in the section on > MALIGN3D in the manual. This works fine for me. The initial alignment > can be obtained with the commands SEQUENCE_TO_ALI and MALIGN. > > Hope this helps, > Oliver > > Mark Daniels wrote: > > Hello all- > > > > I'm trying to run malign3d to align multiple models but the routine > > only 'sees' the first structure and does nothing. I'm using the > > malign3d.top file format described in the Sanchez and Sali 2000 Methods > > in Molecular Biology article: > > > > SET OUTPUT_CONTROL = 1 1 1 1 2 > > SET MAXRES = 700 > > SET ATOM_FILES = 'atip.B99990001' 'atip.B99990002' ; > > 'atip.B99990003' 'atip.B99990004' 'atip.B99990005' > > SET WRITE_FIT = on > > MALIGN3D > > > > All the atip.Bxxxx files contain a reasonable structure. Running the > > malign3d.top routine shown above fails to produce any .fit files and > > shows the following error: > > > > openf5__224_> Open 11 OLD SEQUENTIAL atip.B99990001 > > malign3_327W> Only one structure; nothing done. > > > > Would anyone be able to advise me on what I'm missing here or doing wrong? > > > > Thanks in advance- > > > > Mark Daniels > > The Scripps Research Institute > > > > > > _______________________________________________ > > modeller_usage mailing list > > modeller_usage(a)salilab.org > > http://salilab.org/mailman/listinfo/modeller_usage > > > -- > _______________________________________________________________ > > Oliver Hucke, Dr. > Health Sciences Building - K418C > University of Washington 1959 NE Pacific St. > Dept. of Biochemistry phone: (206) 685 7046 > Box 357742 fax : (206) 685 7002 > Seattle, WA 98195-7742 email: ohucke(a)u.washington.edu > _______________________________________________________________ > > >

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malign3d will not align multiple structures
by Mark Daniels 01 Dec '03

01 Dec '03

Hello all- I'm trying to run malign3d to align multiple models but the routine only 'sees' the first structure and does nothing. I'm using the malign3d.top file format described in the Sanchez and Sali 2000 Methods in Molecular Biology article: SET OUTPUT_CONTROL = 1 1 1 1 2 SET MAXRES = 700 SET ATOM_FILES = 'atip.B99990001' 'atip.B99990002' ; 'atip.B99990003' 'atip.B99990004' 'atip.B99990005' SET WRITE_FIT = on MALIGN3D All the atip.Bxxxx files contain a reasonable structure. Running the malign3d.top routine shown above fails to produce any .fit files and shows the following error: openf5__224_> Open 11 OLD SEQUENTIAL atip.B99990001 malign3_327W> Only one structure; nothing done. Would anyone be able to advise me on what I'm missing here or doing wrong? Thanks in advance- Mark Daniels The Scripps Research Institute

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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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