August 2003 - modeller_usage

Modelling with metals and hetero
by Modeller Care 19 Aug '03

19 Aug '03

non-member submission forwarded by list-owner ------ Forwarded Message Date: Tue, 19 Aug 2003 07:27:56 +0200 From: Tjaart de Beer <tjaart(a)tuks.co.za> Reply-To: tjaart(a)tuks.co.za User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20021204 X-Accept-Language: en-us, en MIME-Version: 1.0 To: modeller_usage(a)salilab.org Subject: Modelling with metals and hetero I have followed the method in the Modeller manual on how to model with water and metals or hetero atoms. The template includes a ligand, metal atom and water molecules. I would like to know how to incorporate this into the newly built model. So far I have succeeded in adding waters during modelling but the metal atom and the ligand is still not in the model. Any help would be greatly appreciated. Thanks!! Tjaart -- Tjaart de Beer Department Biochemistry Agricultural Building Faculty of Natural Sciences University of Pretoria Lynwood rd Pretoria South Africa 0001 Tel: +27 12 420 2990 Cell: +27 83 504 7914 Fax: +27 12 362 5302 Email: tjaart(a)tuks.co.za tjaartdb(a)absamail.co.za ------ End of Forwarded Message

2 1

comparing align. (1 attachment)
by Michael Grabe 18 Aug '03

18 Aug '03

Dear Modellers, I have three published alignments, and I want to use my models generated by Modeller to qualitatively estimate the goodness of the different alignments. I have made 100 models of my unknown sequence to the target structure using each of the three alignments. I then binned the objective energy output from the standard Modeller run (see panel A in attached pdf). I also binned the final C-alpha to C-alpha RMS for the generated models to the known homologous structure (see panel B in attached pdf). Is it true that the energy function is not the best objective measure because different alignments will have different numbers of constraints (i.e. one alignment may correspond to 100 amino acid pairs, whereas a shifted alignment may only have 98 amino acid pairs between the known and unknown sequences.) Can you easily normalize to account for this? What is the best way to do this? I would like to say that Alignment 1 below is best but I am hesitant. Hopefully this question is understandable. Thank you, Michael ------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. Post-doctoral Fellow Howard Hughes Medical Institute University of California, San Francisco 533 Parnassus Ave. San Francisco, CA 94143 mgrabe(a)itsa.ucsf.edu tel: ++ 415.476.6585 http://itsa.ucsf.edu/~mgrabe

1 0

CPIB Tutorial 1
by Andrew Latos 16 Aug '03

16 Aug '03

Hello Andy and Darren, thanks for the help. You were right about the composition of the pdb file containing an acetylated group. This change to the .ali file allowed the models to be generated. >P1;4mdhA structureX:4mdhA: 1 :A: 333 :A:undefined:undefined:-1.00:-1.00 SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEE IAFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKE NFSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFIT TVQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISD-GNSYGVPDDLLYSFPVTIK-DKTWK IVEGLPINDFSREKMDLTAKELAEEKETAFEFLSSA-* >P1;TvLDH sequence:TvLDH: : : : ::: 0.00: 0.00 MSEAAHVLITGAAGQIGYILSHWIASGELYG-DRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPK AAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPE NFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHD-YVFDTFFK KIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIH VVEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG* I appreciate your help. Andrew Latos MBB student University of Idaho

1 0

mutate_model
by Asmat Salim 15 Aug '03

15 Aug '03

Dear MODELLER users I want to mutate a single residue in a model. I run the TOP file given in the tutorial (with 1fas.pdb) successfully. There are two options given: in one case the specified residue is mutated whenever it appears in the structure. This runs fine. But in case of the second option, (where a segment is specified) all the residues are mutated instead of one. Following is the part of the TOP file.( to change residue 14 to Cys) # The second example is commented out; it selects residues '1' and '10'. SET SELECTION_SEARCH = 'SEGMENT', SELECTION_FROM = 'ALL' PICK_ATOMS SELECTION_SEGMENT = '14' '14', SELECTION_STATUS = 'INITIALIZE' # Mutate the selected residues into HSD residues (neutral HIS): MUTATE_MODEL RESIDUE_TYPE = 'CYS' This works perfectly fine with 1fas.pdb but not with my model. Can you point out where I am going wrong. regards

2 1

e-mail
by truename 15 Aug '03

15 Aug '03

Modeller care: I have changed my e-mail from yb_108(a)yeah.net to saint2k2k(a)yahoo.com.cn. please renew my information in the maillist simutaleously. My old mailbox will not be available now bing

1 0

introduction of a Ca binding site
by Karsten Suhre 15 Aug '03

15 Aug '03

Dear Modeller users ! I am trying to model a protein with a Ca binding site, using 7 well aligned structural templates. Some of these structures contain a Ca atom in the homologue position. I read in the documentation that you could introduce hetero atoms and water using a syntax like ASFDGSFA/--WW--W- , but I could not get a hand on a concrete example. Also, if I introduced such a site, would Modeller take the electrostatic interaction between the Ca and the side chain atoms into account in the simulated annealing part? Or would it just place the hetero atoms in the equivalent position? Thank you very much for any suggestion, Kind regards, Karsten -- Karsten Suhre Information Genomique & Structurale CNRS F-13402 Marseille

1 0

Modeller input file
by christos Kouriniadis 09 Aug '03

09 Aug '03

Hi, I am using modeller 6v2. I have the following file: >P1;1sta sequence:1sta:1:@:260:@:aldolase:staca:2.00:-1.00 NQEQFDKIKNGKGFIAALDQSGGSTPKALKDYGVEENEYSNDEEMFNLVHDMRTRIITSPAFNGEKILGAILFEQTMDR EVEGKYTGSYLADKGIVPFLKVDKGLAEEADGVQLMKPIPDLDKLLDRANERGIFGTKMRSNILENNKEAIEKVVKQQF EVAKEIIAAGLVPIIEPEVNINAKDKEAIEANLAEAIKAELDNLKKDQYVMLKLTIPTKVNAYSELIEHPQVIRVVALS GGYSRDEANKILKQNDGLIASFSRALVSDLNAQQSDAEFNEKLQEAIDTIFDASVNKA* I am trying to run modeller for SEARCH, ALIGN2D, MALIGN....commands but everytime I have a reply for wrong command. a). Do I have to save this file into a particular directory? b). Do I have to write mod or mod6v2 together with the file to run the program? Any indication? Christos _________________________________________________________________ MSN 8 with e-mail virus protection service: 2 months FREE* http://join.msn.com/?page=features/virus

1 0

Tutorial from CPIB
by Andrew Latos 05 Aug '03

05 Aug '03

Hello again, Jim, I tried your suggestion of using fewer randomizations to run Modeller but apparently, that was not the problem. I'm now certain that my computer can not handle a full run of Modeller. I've switched over to running the program from a server and that made the first part of the tutorial work. Looking at the example in the manual - as I interpret it - the writer suggests that using 20 randomizations would be good for a trial run but real work would require it to be set to 100. Now I am faced with another problem. I have gone through the example in the first tutorial from http://salilab.org/modeller/user_manual.shtml and am unable to run the model-single.top script. I am wondering why it will not recognize the files in my directory to generate models. It delivers the following error. 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 EBI 6.5 IP30 Date and time of compilation : 07/05/2002 17:12:26 Job starting time (YY/MM/DD HH:MM:SS): 2003/08/05 22:15:20.967 rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 1 1 6 GLY 35 ACE -----GSEPIR check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 7075381 6909.552 6.748 Starting time : 2003/08/05 22:15:20.967 Closing time : 2003/08/05 22:15:24.899 Total CPU time [seconds] : 0.00 Any thoughts as to why the message reads check_a_337 would be appreciated. I am not sure as to why the file is not being found. Thanks. Andrew Latos MMBB University of Idaho PS Antonio Luque: you are running the program without a script file or .top file to tell it what to do. Look up the link above for sample files to work with. The line you type in may look like >c:\modeller6v2\bin\modeller6v2 compare.top I may be wrong about that since I'm not using windows to run the program.

1 0