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
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>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'
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
rathankar rao wrote: > 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
The error is: pdbnam__217W> Filename for PDB code not found: 1ocs
This simply means that your PDB file has the wrong name. It should be called 1ocs.pdb or similar (pdb1ocs.ent, 1ocs.atm are also valid names).
> 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.
There shouldn't be any need to renumber residues in your PDB file. Just make sure you have the correct residue numbering and chain labels in your alignment file.
> 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.
You don't have to do anything special, although you should separate the sequences for the chains in your alignment file by chain break (/) characters.
Ben Webb, Modeller Caretaker