Fwd: Help for "Sequence difference between alignment and pdb"
To: Modeller Usage mailing list <>
Subject: Fwd: Help for "Sequence difference between alignment and pdb"
From: Modeller Caretaker <>
Date: Fri, 26 Sep 2003 18:11:29 -0700
Forwarding to list; please reply to original author.
----- Forwarded message from Dong Chen <> -----
Subject: Help for "Sequence difference between alignment and pdb"
Date: Fri, 26 Sep 2003 18:10:45 -0600
From: "Dong Chen" <>
To: <>
Hi,
I am trying to model a protein by its own structural information, but it
gives me "Sequence difference between alignment and pdb" error message
in the log.file. Could somebody help to see where is problem. Attached
are the files I used.
Thanks,
Dong
####1EDU.atm
####model-Peter.top:
# 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_Peter.ali' # alignment filename
SET KNOWNS = '1EDU' # codes of the templates
SET SEQUENCE = 'peter' # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # 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
####alignment_Peter.ali:
C; A sample alignment in the PIR format; used in tutorial
>P1;1EDU
structure:1EDU:2:A :150:A: : : :
-NIVHNYSEAEIKVREATSNDPWGPSSSLXSEIADLTYNVVAFSEIXSXIWKRLNDHGKNWRHVY
KAXTLXEYLIKTGSERVSQQCKENXYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDR
LREERAHALKTKEKLAQTATA*
>P1;peter
sequence:peter:1 : :150 : : : : :
-NIVHNYSEAEIKVREATSNDPWGPSSSLXSEIADLTYNVVAFSEIXSXIWKRLNDHGKNWRHVY
KAXTLXEYLIKTGSERVSQQCKENXYAVQTLKDFQYVDRDGKDQGVNVREKAKQLVALLRDEDR
LREERAHALKTKEKLAQTATA*
####logfile.log:
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, Windows_NT BTC101DC x86 Family 15 Model 1 Stepping 2, Genuin
Date and time of compilation : Jul 09 2002 16:21:30
Job starting time (YY/MM/DD HH:MM:SS): 2003/09/23 17:56:59.346
TOP_________> 105 705 SET ALNFILE = 'alignment_Peter.ali'
TOP_________> 106 706 SET KNOWNS = '1EDU'
TOP_________> 107 707 SET SEQUENCE = 'peter'
TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files'
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 alignment_Peter.ali
Dynamically allocated memory at amaxbnd [B,kB,MB]: 4458129 4353.642 4.252
openf5__224_> Open 11 OLD SEQUENTIAL alignment_Peter.ali
read_al_374_> Non-standard residue type,position,sequence: X 29 1
read_al_374_> Non-standard residue type,position,sequence: X 46 1
read_al_374_> Non-standard residue type,position,sequence: X 48 1
read_al_374_> Non-standard residue type,position,sequence: X 67 1
read_al_374_> Non-standard residue type,position,sequence: X 70 1
read_al_374_> Non-standard residue type,position,sequence: X 89 1
read_al_374_> Non-standard residue type,position,sequence: X 29 2
read_al_374_> Non-standard residue type,position,sequence: X 46 2
read_al_374_> Non-standard residue type,position,sequence: X 48 2
read_al_374_> Non-standard residue type,position,sequence: X 67 2
read_al_374_> Non-standard residue type,position,sequence: X 70 2
read_al_374_> Non-standard residue type,position,sequence: X 89 2
Read the alignment from file : alignment_Peter.ali
Total number of alignment positions: 149
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1EDU 149 1 1EDU
2 peter 149 1 peter
TOP_________> 121 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND
openf5__224_> Open 11 OLD SEQUENTIAL ../atom_files/1EDU.atm
rdabrk__291E> Sequence difference between alignment and pdb :
STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*-----
1 29 24 UNK 11 MET PSSSLXSEIAD
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]: 4458129 4353.642 4.252
Starting time : 2003/09/23 17:56:59.346
Closing time : 2003/09/23 17:57:01.549
Total CPU time [seconds] : 1.72
----- End forwarded message -----