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

27 Sep 2003


      Hi
more and more new structures are solved using seleno-Met replacements (like your
one as well.)
These Se-Mets become heteroatoms in the PDB structure (HETATM).
Your choices: 
1- "set HETATM_IO= on" in modeller top file and select the protein segment only
(1-150) if you would like to avoid water and other possible ligands (e.g. EGL in
your case) listed after the protein seq in the PDB file. In the sequence you
would use "." for se-METs.
2- replace HETATM records with ATOM records in the PDB file and introduce MSE as
a new residue type (see manual FAQ section for details, which library files to
edit for this, restyp.lib, top_heav.lib etc).
3- do not do anything with the PDB and top files, just leave out Se-MET
positions.  (I.e. In your sequence alignment these will be  gaps in your
template seq). Met residues will be built in your target with more uncertainty 
because no template residue/atoms will be available in those positions.
approach 3 is the quickest but relatively least accurate. Approach 2 is the
biggest hassle but most exact. Approach 1 is in between the previous two in all
regards.
Best wishes,
Andras Fiser
Quoting Xiao-Ping Zhang xpzhang@ucdavis.edu:
> 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
> 
> 
>
-- 
Andras Fiser, PhD, assistant professor
Dept. of Biochemistry & Seaver Center for Bioinformatics
Albert Einstein College of Medicine
1300 Morris Park Ave, Bronx, NY 10461, USA 
phone:(718)430-3233 fax:(718)430-8565