April 2005 - modeller_usage

model refinement and assessment
by Stephen A. Smith 28 Apr '05

28 Apr '05

Hi In MODELLER 7v7 one was able to turn off model refinement using: SET MD_LEVEL = 'nothing' I am curious if there is an analogous way to do this in 8v0? I've looked through the manual and examples and have not found a solution. Have I missed something simple? Is there a way to implement the GA341 and DOPE methods of analysis during the same model building session? I'm also interested in using these analysis methods on other protein models and templates. Is there a quick way to read these models into MODELLER and let it analyze them? Thank you Steve __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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Loops
by John Penniston 27 Apr '05

27 Apr '05

When I attempt to optimize a portion of a molecule for which I don't have a good homolog, the loop optimization procedure always yields a rather nondescript coil with no sheet or helix. Today I tried, as an exercise, to see what "optimization" did to a known crystal structure. I ran the program on the C-terminal helix of calmodulin, a molecule for which the structure is very well known. As has been my experience before, the result was destruction of that nice orderly helix, which was replaced by a coil going off in no particular direction. Can anyone tell me why this happens, and how I can use this procedure to get a better result? Thanks. John Penniston

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MODELER v6.3 script
by O'MAHONY, BRIAN 27 Apr '05

27 Apr '05

I am trying to refine a loop region in my protein using "select atoms". The roblem is I only have the manual for version 4 and many variables have been redefined. Can someone tell me the script or better still send me the manual for version 6.3. I can't find it on the net Brian O'Mahony Institut Municipal de Investigació Mèdica (IMIM) Pharmacology Research Unit Dr. Aiguader, 80 E-08003 Barcelona, Spain Tel: +34 - 93 225 25 97 E-mail: mailto:bomahony@imim.es Web: http//www.imim.es

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Multidomain protein
by Ranjit Kumar 25 Apr '05

25 Apr '05

Dear Sir, I am trying to model a protein which has three domains seperated by linker region in a linear fashion.Domain are not overlapping as they are seperated by linkers.By macromolecular docking I generated their best possible orientation and used as input PDB files.But the model given by modeller wont preserve the provided orientation and domain got seperated further by the linker regions.The template for linker region has streches of helixes seperated by coils. So what should I do to preserve the domain orientation and then generate the possible model or I should use any other approach? Waiting for your reply.... Research Student Ranjit Kumar

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An error with final_malign3d
by Mensur Dlakic 25 Apr '05

25 Apr '05

Hi, This error occurs both with Windows and Linus versions of Modeller 8v0 when 'a.final_malign3d = True' is left in the script file. If this statement is commented out and the script is otherwise unchanged, it works just fine. The job gets stopped right at the very end, presumably before the models are fitted to the template. Similar thing happens when these two lines are in the script: mdl = model(env) mdl.optimize(optimization_method=3, max_iterations=50, output='REPORT', trace_output=1) In this case, however, the script dies at the beginning. Again, commenting out these two statements is all it takes to get the job going. I'll send the error messages to Ben only, the whole list probably doesn't need to see them. Any suggestion/advice is appreciated. Cheers, Mensur ========================================================================== | Mensur Dlakic, PhD | Tel: (406) 994-6576 | | Department of Microbiology | Fax: (406) 994-4926 | | Montana State University | | | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur | | Bozeman, MT 59717-3520 | E-mail: mdlakic(a)montana.edu | ==========================================================================

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pick.atoms
by jean-marc vuissoz 25 Apr '05

25 Apr '05

hello, I would like to do a selection of many atoms ( 45-46, 110-112, 147-149), but I don't manage to do it, how should I dot it ? best tanks jean-marc # select_loop_atoms (necessary) class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): # 4 residue insertion (1st loop) self.pick_atoms(selection_segment=('147:', '149:'), selection_status='INITIALIZE')

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prb encountered, plz help
by rathankar rao 24 Apr '05

24 Apr '05

i had to model a protein whose ali file, top file and the log files are present here. i couldnt model it and its always presenting some or the other errors plz help there was one problem in the pdb file,: a ligand cme under the name of the heteroatom, had a residue number as 91 , which was supposed to be a number for the aminoacid. the next residue thus continued from 92 and so on. so i changed the residue numbers by 1. i changed the ligand atom number also as 1191 instead of 91 so that it is distinguished from the other aminoacids. despite all these it dosent work. i have one more doubt , if at all the protein as many chains then how do i model it. what is the command which is used to model a protein with chains. plz explain with regadrs rathankar __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com >P1;1ocs structureX:1ocs:30:A:160:A:yhr: yeast:2.03:0.217 AEPENFLEIEVHNPKTHIPNGMDSKGMFTDYEIICRTNLP------SFHKRVSKVRRRYSDFEFFRKLIKEISML NHPKV----MVPHLPGKILLSN-------RFSNEVIEERRQGLNTWMQSVAGHPLLQSGSKVLVR-FIEAEKFV* >P1;yhr sequence:yhr:1: :149: :yhr: yeast: 2.00: -1.00 SINANFSFQKAHVSDCTIVNG-DHGTKFAVWRITVFLEPNLKAFAAKRESYKIQTYKRYSDFVRLRENLLTRIKT AKPEKLNCLQIPHLPPSVQWYSSWKYQEVNLNKDWLAKRQRGLEYFLNHIILNSSLVEMTKDILIQFLEPSKRV* # Fichier d'entree pour la procedure 'model' INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'yhr.ali' SET KNOWNS = '1ocs' # SET SEQUENCE = 'yhr' # SET ATOM_FILES_DIRECTORY = './:../atom_files' SET STARTING_MODEL= 1 SET ENDING_MODEL= 1 CALL ROUTINE = 'model' MODELLER 7v7, Sep 12, 2004 09:15pm PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2004 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA 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, WinME build 4114, TJAY-4, uni, x86 Family 6 Model 3 Stepping 0 Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2004/04/25 20:21:56.690 TOP_________> 109 749 SET ALNFILE = 'yhr.ali' TOP_________> 110 750 SET KNOWNS = '1ocs' TOP_________> 111 751 SET SEQUENCE = 'yhr' TOP_________> 112 752 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 113 753 SET STARTING_MODEL = 1 TOP_________> 114 754 SET ENDING_MODEL = 1 TOP_________> 115 755 CALL ROUTINE = 'model' TOP_________> 116 419 CALL ROUTINE = 'getnames' TOP_________> 117 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 118 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 119 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 120 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 121 538 SET ROOT_NAME = SEQUENCE TOP_________> 122 539 RETURN TOP_________> 123 420 CALL ROUTINE = 'homcsr' TOP_________> 124 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL yhr.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 2743707 2679.401 2.617 openf5__224_> Open 20 OLD SEQUENTIAL yhr.ali Read the alignment from file : yhr.ali Total number of alignment positions: 149 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1ocs 131 1 1ocs yhr 2 yhr 148 1 yhr yhr TOP_________> 125 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 126 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND pdbnam__217W> Filename for PDB code not found: 1ocs Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 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]: 2743857 2679.548 2.617 Starting time : 2004/04/25 20:21:56.690 Closing time : 2004/04/25 20:22:01.300 Total CPU time [seconds] : 4.61

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Python interpreter with Modeller 8v0
by gerald.quon＠utoronto.ca 22 Apr '05

22 Apr '05

Hi, I'm trying to use basic python commands with modeller 8, but am finding the commands are simply ignored. I'm mainly interested in using the 'import' command so i can build a small library of functions for use with MODELLER scripts, but the import command doesn't seem to be working for me - has anyone tried it? If not, I'm wondering if it's possible to use a standard python interpreter for say, linux, instead of the MODELLER interpreter. Thanks! Gerald

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potassium ion
by fredrik 18 Apr '05

18 Apr '05

Hi, I have a template with a potassium ion and I'm trying to use it in my modelling. What I can see from the manual and file code I should use: % in the .ali MK as atom name in the .pdb K as residue name in the .pdb ATOM instead of HETATM in the .pdb This how ever doesn't work. I have tried to use e.g. zinc ion and that work (z, ZN2, ZN2 resp.). I would be very great full for any help! Regards, Fredrik.

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Modeller 8v0 release
by Modeller Caretaker 18 Apr '05

18 Apr '05

The new version of Modeller, 8v0, is now available for download from http://salilab.org/modeller/. If you have a license key for Modeller 7v7, there is no need to reregister for Modeller 8v0 - the same license key will work. (It won't do any harm to reregister if you want to, though!) If you encounter bugs in Modeller 8, please see http://salilab.org/modeller/manual/node11.html for information on how to report them. New features in Modeller 8 include: # TOP is no longer used as the scripting language. MODELLER now reads Python 2.3 scripts instead. (TOP scripts can still be used, but will not take advantage of all new features.) See Chapter 4 for more information. # Incorporation of the GA341 (model.assess_ga341()) and DOPE (model.assess_dope()) methods for model assessment. # `Automatic' filename generation (when filenames were set to 'default') is no longer supported; use the modfile.default() function instead. # Memory is used much more efficiently, and various limits evident in older releases (e.g., errors concerning MAXRES, MAXCNS and MAXBND) have been removed. Consequently, you can no longer assign to the MAXRES variable; this is not necessary now. # New alignment.salign() alignment command, using structural information, and based on the COMPARER program. # Various fixes to profile.build(), and a new command profile.scan(), for building and using sequence profiles. # Generated models can be docked to electron microscopy density maps, using the new density.grid_search() command. # Superpositions are now improved by using local substructures. This local refinement can be disabled (thus getting the behavior of old MODELLER versions) by turning off the refine_local option to model.superpose(). # MODELLER will now read compressed files in the .gz and .bz2 formats (as well as the existing .Z format) provided the gzip and bzip2 programs are available. # Fixes for various problems reading alignment files with very long lines, or with Mac, Unix or DOS-style line endings. # Bug fix for alignment.compare_structures(); disulfide bridges were not being properly considered in the comparison. # Charges for all topologies are now assigned using a `nearest neighbor' technique; see topology.make(). # sequence_db.search() (formerly SEQUENCE_SEARCH) now takes a 1-sequence alignment as input, rather than reading in that alignment itself. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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