October 2002 - modeller_usage

Bug reported in previous message - Description and Workaround
by Richard Friedman 21 Oct '02

21 Oct '02

Dear Modeller Team, I am running Modeller 6v2 on a Dec Alpha. I was not able to run the compare script for the TvLDH tutorial successfully with the script and filenamse provided. The directory in which I attempted this is encoded in the preceeding e-mail message. As far as I can see, the program is reading the input pdb file name incorrectly. For example, 1bmdA is read as 1bmd. As a result the job does not run. I found however when I copied the pdb files to ones with shorter names i.e. copied 1bmdA.pdb to 1bmd.pdb the script ran well. Please excuse me if this apparent bug is really due to an error on my part, but if it is, please let me know how. Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.ccc.columbia.edu http://cancercenter.ccc.columbia.edu/~friedman/ In Memoriam, Robert Kanigher

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Problem to modeller
by Juan Palacios 18 Oct '02

18 Oct '02

What is a problem?? i need help... 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, Linux bioinf4 2.4.4-4GB i686 Date and time of compilation : 05/24/2002 09:27:23 Job starting time (YY/MM/DD HH:MM:SS): 2002/10/17 15:00:00.125 TOP_________> 105 705 SET ALNFILE = '1f4h-so34a0.ali' TOP_________> 106 706 SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta' TOP_________> 107 707 SET KNOWNS = '1f4hD' TOP_________> 108 708 SET SEQUENCE = 'so34a0' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL 1f4h-so34a0.ali openf5__224_> Open 13 OLD SEQUENTIAL /home/jpalacio/fasta/pdb1f4h.ent rdpir___270E> Error reading/processing file: 1f4h-so34a0.ali recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2205269 2153.583 2.103 Starting time : 2002/10/17 15:00:00.125 Closing time : 2002/10/17 15:00:03.672 Total CPU time [seconds] : 3.36 ---------------------- teha align file is: >P1;1f4hD structureX:1f4h: :D:: :::: ITDSLAVVLQRRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAWFPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN* >P1;so34a0 sequence:so34a0: : : : ::: 0.00: 0.00 KFNSRAGVLQRGDVENPGVAQLNRLGEHPLFASWRNSEEARTGSPFLQVGSLNGKWDAPCSGALNEGPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVN* -------------------------- the top file: # 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 = '1f4h-so34a0.ali' # alignment filename SET ATOM_FILES_DIRECTORY = '/home/jpalacio/fasta' SET KNOWNS = '1f4hD' # codes of the templates SET SEQUENCE = 'so34a0' # code of the target SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling ----------------------------

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Question on 1fdx example
by Richard Friedman 18 Oct '02

18 Oct '02

Fellow Modellers, I ran the first example in the Modeller tutorial, 1fdx, and I got several restraint violations in the final structure. I ran the diagnostics, and I dod not receive any error messages. Is this as it should be? Is there anywhere in which one can obtain a standard 1fdx run that can be used as a "known"? I know that, based upon faq #23, interpreting restraint violations is something of an art. I am asking to make sure that I ran the program correctly, and that the program is running as it should be. My violated restraints are: Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 379 0 0 0.005 0.005 2.8642 1.000 2 Bond angle potential : 520 0 0 2.444 2.444 59.089 1.000 3 Stereochemical cosine torsion poten: 244 0 10 55.593 55.593 103.81 1.000 4 Stereochemical improper torsion pot: 146 0 0 1.474 1.474 6.3455 1.000 5 Soft-sphere overlap restraints : 663 0 0 0.002 0.002 0.47318 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 804 0 0 0.344 0.344 30.114 1.000 10 Distance restraints 2 (N-O) : 832 0 1 0.467 0.467 37.873 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 53 0 0 4.634 4.634 13.423 1.000 14 Sidechain Chi_1 dihedral restraints: 43 0 1 72.693 72.693 11.147 1.000 15 Sidechain Chi_2 dihedral restraints: 26 0 1 68.739 68.739 16.513 1.000 16 Sidechain Chi_3 dihedral restraints: 9 0 0 37.987 37.987 3.4346 1.000 17 Sidechain Chi_4 dihedral restraints: 1 0 0 124.535 124.535 1.0173 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 553 0 0 0.540 0.540 18.286 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 52 9 5 29.961 67.309 9.4985 1.000 26 Distance restraints 4 (SDCH-SDCH) : 100 0 2 1.196 1.196 15.584 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 openf5__224_> Open 17 UNKNOWN SEQUENTIAL 1fdx.V99990001 # Heavy relative violation of each residue is written to: 1fdx.V99990001 # The profile is NOT normalized by the number of restraints. # The profiles are smoothed over a window of residues: 1 List of the violated restraints: A restraint is violated when the relative difference from the best value (RVIOL) is larger than CUTOFF. ICSR ... index of a restraint in the current set. RESNO ... residue numbers of the first two atoms. ATM ... IUPAC atom names of the first two atoms. FEAT ... the value of the feature in the model. restr ... the mean of the basis restraint with the smallest difference from the model (local minimum). viol ... difference from the local minimum. rviol ... relative difference from the local minimum. RESTR ... the best value (global minimum). VIOL ... difference from the best value. RVIOL ... relative difference from the best value. ------------------------------------------------------------------------------------------------- Feature 25 : Phi/Psi pair of dihedral restraints List of the RVIOL violations larger than : 6.5000 # ICSR RESNO1/2 ATM1/2 INDATM1/2 FEAT restr viol rviol RESTR VIOL RVIOL 1 1296 7S 8C C N 53 55 -75.51 -117.90 43.16 1.34 -63.00 174.54 20.46 1 8C 8C N CA 55 56 133.00 141.10 -41.10 2 1297 8C 9I C N 59 61 -109.33 -97.30 83.47 8.55 -63.40 99.45 15.16 2 9I 9I N CA 61 62 44.60 127.20 -43.60 3 1298 9I 10A C N 67 69 43.10 55.40 23.15 0.89 -62.50 144.55 28.99 3 10A 10A N CA 69 70 57.81 38.20 -40.90 4 1299 10A 11C C N 72 74 -61.78 -63.00 1.43 0.25 -117.90 -172.86 8.06 4 11C 11C N CA 74 75 -40.37 -41.10 141.10 5 1310 21N 22I C N 146 148 -109.14 -120.60 69.78 3.55 -63.40 114.60 17.55 5 22I 22I N CA 148 149 61.47 130.30 -43.60 6 1313 24Q 25G C N 171 173 98.62 78.70 39.64 0.60 82.20 152.01 8.20 6 25G 25G N CA 173 174 159.62 -166.10 8.50 7 1314 25G 26S C N 175 177 -65.61 -64.10 21.61 1.66 -136.60 167.99 9.49 7 26S 26S N CA 177 178 -56.55 -35.00 151.20 8 1315 26S 27I C N 181 183 -64.03 -63.40 6.55 1.10 -120.60 -171.73 12.88 8 27I 27I N CA 183 184 -50.13 -43.60 130.30 9 1316 27I 28Y C N 189 191 104.14 -124.30 131.89 10.18 -124.30 131.89 10.18 9 28Y 28Y N CA 191 192 126.16 135.40 135.40 Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman(a)cancercenter.ccc.columbia.edu http://cancercenter.ccc.columbia.edu/~friedman/ In Memoriam, Robert Kanigher

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modeller usage
by Somanadh Babu 17 Oct '02

17 Oct '02

Hello, I am a begiiner with modeller. I am using modeller6v2. I tried running modeller with model-default.top as the input file and from what I knew,a '.atm' file has to be generated after the process. I am working in LINUX. The process stopped after a couple of seconds and the message STOP was thrown. No ".atm" file was generated. How do I proceed further? sincerely, somanadh

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Problems reading in pdb template file
by Ralph Elison 16 Oct '02

16 Oct '02

Hi, I'm quite new to using MODELLER and am having difficulties reading in a pdb template file. Judging from the log file, I've been able to read in the A chain of 1hzx, bovine rhodopsen, but later get a complaint that no atoms were read from the specified file. Can someone please give a hint as to what the problem is? Below is my top file and the relevant output from the log file. Thanks, Michael Moser INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 0 SET ALNFILE = 'protstruct3.ali' SET KNOWNS = '1hzx' READ_MODEL FILE = '1hzx', MODEL_SEGMENT = 'FIRST:A' 'LAST:A' SET SEQUENCE = 'jegA' SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL= 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' # do homology modelling TOP_________> 107 707 READ_MODEL FILE = '1hzx', MODEL_SEGMENT = 'FIRST:A' 'LAST:A' openf5__224_> Open 11 OLD SEQUENTIAL ./1hzx.atm openf5__224_> Open 11 OLD SEQUENTIAL ./1hzx.atm rdatm___297_> Segments, residues, atoms: 1 340 2681 rdatm___298_> Segment: 1 1 A 1 A 2681 TOP_________> 108 708 SET SEQUENCE = 'jegA' . . . . Read the alignment from file : protstruct3.ali Total number of alignment positions: 381 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1hzx 348 1 1hzx 2 jegA 371 1 jegA unknown TOP_________> 122 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1hzx.atm rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specified. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 1: To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 348 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 __________________________________________________ Do you Yahoo!? Faith Hill - Exclusive Performances, Videos & More http://faith.yahoo.com

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problem with SET MD_LEVEL
by Frank J A B 15 Oct '02

15 Oct '02

Dear Users Recently, I was facing a problem when I try to set the MD_LEVEL = 'refine1' instead of using it as 'nothing' (which works normally) After a dozen of minutes, the log file returns the following ... TOP_________> 469 273 SET MAX_ITERATIONS_STORE = MAX_ITERATIONS TOP_________> 470 274 IF ARGUMENTS = REFINE_HOT_ONLY 1, OPERATION = 'NE', THEN ; 'GO_TO __BEGIN_MD' TOP_________> 471 285 CALL ROUTINE = MD_LEVEL act10___551E> No such routine: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I've installed the mod6v2 both in a Octane2 (IRIX6.5) and in a PC with Linux RedHat and still face the same problem. I don't remember that other user had commented that we must to set something special (a variable or so) to run MD in our models. Any hint will be very helpful Thanks in advance Frank Alarcon www.lncc.br

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problem with SET MD_LEVEL
by Frank J A B 14 Oct '02

14 Oct '02

Dear All/Bozidar I've just corrected the .top script with the underscore in refine_1 (instead of the 'refine1' mentioned in the script itself) and got this message. assgn___544E> Variable name not recognized: /pipe1/databases/pdb/uncompressed_files/pdb1hci.ent Command line: INCLUDE assgn___525E> Error in TOP variable assignment. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I reinforce that I use the same script whitout any problem. Any help will be very welcome Thanks again Frank Alarcon

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(no subject)
by Santiago Ramon 13 Oct '02

13 Oct '02

Dear modellers: I have modelled a molecule successfully using modeller. This molecule forms dimers, probably very similar as it occurs with the template molecule, and I would like to optimize my model to improve the dimerization surface and intersubunit contacts. Which would be the best strategy to do it so?. How can I restrain changes in one subunit to be exactly modelled in the other subunit?. Many thanks in advance for your suggestions, Santiago *********************************************** Santiago Ramón-Maiques Instituto de Biomedicina de Valencia Consejo Superior de Investigaciones Científicas C/ Jaime Roig, 11 46010 Valencia, Spain ***********************************************

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PDB format problem...
by 유아림 12 Oct '02

12 Oct '02

Hi Modellers! I have the pdb format problem. I have the same problem with Stephane Coillet-Matillon's error written at 19 Mar 2002. Eric Feyfant replied it was a chain identifier problem. " I corrected Stephane error. It was a chain identifier problem. The chain was specified in the pdb but not in the top file, and Modeler could not extrapolate. Eric" But I don't know how to correct this problem. How to solve this problem? Thanks, Ahrim The error messages is like this " Read the alignment from file : acc_ipn1.ali Total number of alignment positions: 375 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1QJF 331 1 1QJF 2 ACCO 314 1 ACCO unknown TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1QJF.pdb rdpdb___303E> No atoms were read from the specified input PDB file: 1) Possibly because an incorrect/non-existent PDB file is specif ied. 2) Possibly because the segment is specified incorrectly in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the beginning residue number and/or chain id in MODEL_SEGMENT may not be found in the input PDB file; MODEL_SEGMENT: 1: To find out more, switch on maximal output by 'SET OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 331 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 " YOO, AHRIM Process System Lab. Department of Chemical Engineering, Korea University --------------------------------------------------------------------------------------- Don't believe what your eyes are telling you. All they show is limitation. Look with your understanding, find out what you already know, and you'll see the way to fly.

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Atom index out of range
by Satyan Sharma 11 Oct '02

11 Oct '02

Hi Modeller users, I am trying to model a 2 domain protein. I give a pdb file with 2 chains (toatal of 1828 atoms)along with the alignment. During the run I get an error - Atom index is out of range. nselat__596E> Atom index is out of range (iatm,natm): 1829 1828 Any idea what could be wrong Cheers, Satyan

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