September 2002 - modeller_usage

stuck
by Jory L. Zmuda 15 Sep '02

15 Sep '02

will someone please help me. I would like to use Modeller to align the structures of 41 protein sequences to 1E1E, which has a structure. I have PDB files of all 42 proteins, and I have aligned all of them using ClustalW. I have altered the alignment to the PIR format, as specified. I am trying to perform an initial family alignment of all structures and sequences, as specified in 1.7.2, yet MALIGN3D does not work. It will not read in the structural information. I am very confused by everything and would greatly appreciate if someone could help me go through the process of aligning protein sequences to a known structure.

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Bounced emails
by Bozidar Yerkovich 06 Sep '02

06 Sep '02

Hi all, I wanted to remind you once again that if you submit an email to the modeller_usage list it MUST be from the same email account a the one you used to sign up yourself from, otherwise your submission will get bounced back. Happy modeling, Bozidar

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Re: Modeller for Mac OS X
by Bozidar Yerkovich 03 Sep '02

03 Sep '02

Hi Dhaval, Although it shouldn't be, it might be ;-) Make sure you are in tcsh. If that doesn't help I would suspect it's Jaguar. I have compiled this version of MODELLER on my PowerBook running 10.1.5. Best, Bozidar > Hi Bozidar > > I'm sorry to bother you again, I've tried to run the Install script > but my computer refuses to open it. It claims it can't open it > because it of a disk error. I am running the new OS X 10.2, do you > think this might be the source of the problem?

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'sequence not read in'
by 조병관 03 Sep '02

03 Sep '02

Hi modellers.. Today, i met this message from modeller....but i can not understand why this occurs.... i retrived 3TAT.pdb file from www.pdb.org and prepared ate1.ali file from ClustalW in PIR format... The related files and log file are below.... why modeller give me the 'sequence not read in' message?? Byung-Kwan - ate1.ali file >P1;ate1 sequence:ate1:1: :397: :ArATEs:Enterobacter_sp: : MFQKVDAYAGDPILSLMER.....QRVAQAFAAVM* >P1;3TAT sequenceX:3TAT: :A: :A:ArATEc:Escherichia_coli: : MFQKVDAYAGDPILTLMER.....QRVAKAFAAVM* - 3TAT.pdb - ate1.top # Homology modelling by the MODELLER TOP INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'ate1.ali' SET KNOWNS = '3TAT' SET SEQUENCE = 'ate1' SET ATOM_FILES_DIRECTORY = '/usr/bin/modeller6v1/examples/tutorial-model/atm/' SET STARTING_MODEL= 1 SET ENDING_MODEL= 5 SET RAND_SEED = '76077' SET MD_LEVEL = 'refine1' CALL ROUTINE = 'model' - ate1.log MODELLER 6v1, 17 Jan 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 localhost 2.2.18-10 i686 Date and time of compilation : 01/24/2002 16:28:15 Job starting time (YY/MM/DD HH:MM:SS): 2002/09/03 13:59:14.415 TOP_________> 105 705 SET ALNFILE = 'ate1.ali' TOP_________> 106 706 SET KNOWNS = '3TAT' TOP_________> 107 707 SET SEQUENCE = 'ate1' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 5 TOP_________> 111 711 SET RAND_SEED = '76077' TOP_________> 112 712 SET MD_LEVEL = 'refine1' TOP_________> 113 713 CALL ROUTINE = 'model' TOP_________> 114 398 CALL ROUTINE = 'getnames' TOP_________> 115 508 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 116 509 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 117 510 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 118 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 119 512 SET ROOT_NAME = SEQUENCE TOP_________> 120 513 RETURN TOP_________> 121 399 CALL ROUTINE = 'homcsr' TOP_________> 122 106 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 ate1.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 7974421 7787.521 7.605 openf5__224_> Open 11 OLD SEQUENTIAL ate1.ali Read the alignment from file : ate1.ali Total number of alignment positions: 397 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 3TAT 397 1 3TAT ArATEc 2 ate1 397 1 ate1 ArATEs TOP_________> 123 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND 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]: 7974421 7787.521 7.605 Starting time : 2002/09/03 13:59:14.415 Closing time : 2002/09/03 13:59:15.159 Total CPU time [seconds] : 0.70

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atom file
by 조병관 02 Sep '02

02 Sep '02

Hi modellers.. When i run modeller6v1, i met 'sequence not read in' message in .log file... There are not any problems in .ali file.... If the known sequence residue number is different with its residue number in PDB file, how can i edit the PDB file ? e.g. .ali file MFMKF...... .pdb file M 5 F 6 M 10 ...... Regard.. Byung-Kwan Cho

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2 problems - HETATM_IO and strange log (fwd)
by Frank J A B 02 Sep '02

02 Sep '02

Dear All I'm facing to problems with modeller. In the FAQ's question #16 there is an explanation on how to use hetero atoms in modelling adding the line HETATM_IO = on in the top script. There is also a comment (confuse in my opinion) about the use of w for water and . for other atoms in the alignment that still remains unsolved to me. In my case I'm trying to use FAD in the modelling. I can't wonder how to edit the alignment to include this Ws and .s Check the example given. INCLUDE SET ALIGNMENT_FILE = 'align1.ali', KNOWNS='templ1', SEQUENCE='targ1' SET HETATM_IO = on, WATER_IO = on CALL ROUTINE = 'model' The alignment file: >P1;templ1 structureX:templ1:1::10:: FAYVI/.wwww* >P1;targ1 sequence:targ1:1::8:: -GWIV/.ww-w* Need I to repeat the entire alignment (template/target) inside the same .pir file, but now only with signs like - , ., w , #) where the .s/Ws positions correpond to those aa that make contact with the HETATM in the structure/template ? The second question is about my log file. I'm habituated to use regularly Modeller since version 4 but suddenly the job was finished abruptly with this : MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS 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 Is this some kind of bug or a user error ? I'm sure that the files are typed correctly (case-sensitive) and the folder where the job is started has all the files in it. Any hint asap will be very much appreciated. Thanks in advance brgds Frank Alarcon LNCC - Brasil www.lncc.br

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