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Re: Fwd: Help for "Sequence difference between alignment and pdb"



Dear Dong,

You should replace the "X" with its real code. It might be M (Met).

Good luck.

Xiao-Ping



At 06:11 PM 9/26/2003 -0700, you wrote:
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 -----

Xiao-Ping Zhang, PhD
Section of Microbiology
Division of Biological Sciences
University of California, Davis
Davis, CA95616