January 2002 - modeller_usage

malign3D question
by Karen C. Ellis 24 Jan '02

24 Jan '02

I was trying to use the malign3D command to do an alignment of three sequences based on their PDB structures. I was able to get an inital alignment from the command malign with no problems. I used this alignment as the starting point. I then copied the commands found on the user manual page for malign3d (of course changing the file names as appropriate) to a .top file. When I look at the .log file I get the following error fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 I have also tried running align3d for two sequences at a time and that works fine. Any suggestions on what I am doing wrong? Thanks, Karen Ellis

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Error using MALIGN3D
by Michael Buck 24 Jan '02

24 Jan '02

MALIGN3D Top files which worked well using Modeler 4 are giving me this error : fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am using the following script # MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off If anybody has seen this problem, please help. Thank you Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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RE: SS bridges
by Andrej Sali 24 Jan '02

24 Jan '02

Thanks, Roberto, it was a bug in the source code. Fixed now, will put a new version on the web in a day or two. Thanks, Andrej -- Andrej Sali, Associate Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali(a)rockefeller.edu; http://salilab.org -----Original Message----- From: Roberto Sanchez [mailto:Roberto.Sanchez@mssm.edu] Sent: Thursday, January 24, 2002 1:15 AM To: sali(a)rockefeller.edu Subject: SS bridges Andrej, We also observed recently the problem with the SS bridges in mod6. Manual patching works, but SS's from the template do not get formed. So if you need another test case let me know. Best, Roberto -- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/

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disulfides
by Daniel John Rigden 23 Jan '02

23 Jan '02

Hi Is there a problem with automatic disulfides in Modeller 6? My recent models are being produced without the disulfides present in the templates and I don't remember this being a problem with earlier versions. In the log file there is a call to the relevant patch routine TOP_________> 151 465 PATCH_SS_TEMPLATES but it doesn't seem to work. The template files have been processed so that they have lost PDB headers but I assume MODELLER figures SS bonds for itself rather than reading SSBOND lines in PDB headers... We can always define the disulfides manually with the general PATCH command but, as the manual says, they'll be better defined by PATCH_SS_TEMPLATES - generated restraints. Thanks for your help. Daniel +-------------------------------------------------------------------------+ | Dr Daniel John Rigden | | CENARGEN/EMBRAPA | e-mail: daniel(a)cenargen.embrapa.br | | Parque Estacao Biologica | http://www.cenargen.embrapa.br | | PqEB - Final - Av. W3 Norte | Phone: +55 (61)448-4741 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3658 | +-------------------------------------------------------------------------+

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SEQUENCE_COMPARISON
by Obdulia Rabal 22 Jan '02

22 Jan '02

Hello. I am trying to use the command: SEQUENCE_COMPARISON, but I don´t understand the output, in the MATRIX_FILE. I mean, I don´t know what each number means ( which one is the score which I can use to compare different alignments) For example, thix matrix is the result when I use : RR_FILE = '$(LIB)/gonnet.sim.mat' and my alignmet. sequenceA 514.40 297.72 sequenceB 297.72 504.86 I suposse the score I have to compare is 297.72 (which changes in different alignments). My problem is that I am using another aligment server, with the same parameters I use in Modeller , and it gives only the score 504. Thanks in advance

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starting problem
by Boojala Reddy 20 Jan '02

20 Jan '02

Hi.. I am getting following when I first tried the tutoraial: ============== palomar (117) % mod6v0 model-default sys-2 : UNRECOVERABLE error on system request No such file or directory Encountered during an OPEN of unit 11 Fortran unit 11 is not connected IOT Trap /projects/nbcr/breddy/SOFTWARE/MODELLER/MODELLER6v0/modeller6v0/bin/mod6v0[41]: 495462 Abort ================== Please help: my modified tops file where I only changed the atom file directory -------------- # 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 = 'alignment.ali' # alignment filename SET KNOWNS = '5fd1' # codes of the templates SET SEQUENCE = '1fdx' # code of the target SET ATOM_FILES_DIRECTORY = '/projects/nbcr/breddy/SOFTWARE/MODELLER/MODELLER6v0/TEST' # directories for input atom files 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 about log files
by Xavier Gallet 17 Jan '02

17 Jan '02

Hi, My last Modeller job failed, and the last line of my log file is: coutpir___E> reading in alignment Can you tell me what 'coutpir' means ?? More generally, where can I find a list of Modeller error messages and their significances. Thanks in advance, Xavier Gallet, PhD Department of Bioinformatics & IT GenOdyssee S.A. 3 avenue du Canada Batiment Alpha, Porte 6 B.P. 810 Les Ulis 91974 Courtaboeuf Cedex, France e-mail : gallet(a)genodyssee.com website: http://www.genodyssee.com

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select_loop_atoms
by Obdulia Rabal 17 Jan '02

17 Jan '02

Hi, I have a problem with the __loop.top. When I try to run it with the following 'selected atoms': SUBROUTINE ROUTINE = 'select_loop_atoms' READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUENCE, ADD_SEQUENCE = off SET SELECTION_STATUS = 'INITIALIZE' SET SELECTION_MODE = 'ATOM' SET SELECTION_SEARCH = 'SEGMENT' SET SELECTION_FROM = 'ALL' SET GAP_EXTENSION = 2 2 # gaps are extended for two residues in both # directions to get loops (insertions & deletions) PICK_ATOMS SELECTION_SEGMENT = 'LOOPS' RETURN END_SUBROUTINE it seems to select all the atoms in the model (that's what I see when it does UNBUILD_MODEL, because all the coordinates are put to -999). I don`t understand why it does it, because it should only choose atoms aligned with gaps +/- 2 ( insertions or deletions). Do I have wrong ideas? If not, what's the best way to choose atoms in the __loop.top? ( I would like to do it automatically, not by choosing every time the segment). Thanks in advance.

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Question
by Paolo Daniele 16 Jan '02

16 Jan '02

Hi, I have a problem. Using Modeller program to make 100 models of my protein following the loop routine, the program was stopped because of an electric interruption, so I have now just 56 of 100 models! Is there a way to restart the program without loosing the 56 models yet obtained? Thanks in advance for your help. Best regards, Paolo Daniele ______________________________________________________________________ Iscriviti al gruppo ufficiale di Tomb Raider: http://it.groups.yahoo.com/group/gruppoufficiale_tombraider/

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Potential energy calculations with MODELLER
by Francois Sampieri 16 Jan '02

16 Jan '02

Hi and Greetings to all ! I used MODELLER to generate a huge number (3500 pdb files) of models of the same protein with 7 different disulfide pairings (500 models of each pairing), and now I have to sort the models according their potential energies (bonded + non-bonded) in vacuum. I initially thought of using a molecular mechanics software in standalone mode to be lauched on each pdb file by a perl script, and then collect the energy values in whatever format the software created. I start looking for such a program which should be: - executable for SGI 02 R10K (IRIX 6.5); - free for academics; - launchable from a Perl script; But I didn't found such a jewel (oh no!, not such of highest value as MODELLER!) on the Web. So I come back to MODELLER, though its top script mode didn't seem the simplest way to me to achieve batch energy calculations, but I hope I'm wrong. Could anybody suggest a method to use MODELLER for computing (CHARMM) potential energy of billions of structures in pdb format? Many thanks in advance! François Sampieri ____________________________________________ UMR 6560 CNRS-Universite de la Mediterranee Laboratoire de Biochimie - IFR Jean Roche Faculte de Medecine Nord Bd Pierre Dramard 13916 Marseille Cedex 20 E-mail: sampieri.f(a)jean-roche.univ-mrs.fr Fax: (33) 4 91 65 75 95 Tel: (33) 4 91 69 88 44

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