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 dong.chen@usu.edu ----- > >Subject: Help for "Sequence difference between alignment and pdb" >Date: Fri, 26 Sep 2003 18:10:45 -0600 >From: "Dong Chen" dong.chen@usu.edu >To: modeller-care@salilab.org > >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