Re: Alignment problem

[Bozidar Yerkovich <>]

Frederico,

Please check if your ali file is in the right directory?
You are simply not reading the file in....

Best,
Bozidar



On Thu, 18 Jul 2002, Frederico Moreno wrote:

> Dear Bozidar,
> 
> I had problem when trying to get some a protein model.
> What do I have to do? I used the PIR alignment format
> also.
> 
> My Top file is:
> 
> INCLUDE                             # Include the
> predefined TOP routines
> 
> SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to
> produce a large log file
> SET ALNFILE  = 'alignment.seg.pap'      # alignment
> filename
> SET KNOWNS   = '1h9p'               # codes of the
> templates
> SET SEQUENCE = '1drg'               # 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
> 
> The alignment file seems to be ok:
> 
> 
> Kind, OS, HostName, Kernel, Processor: 4, Linux
> localhost.localdomain 2.4.18-6mdkenterprise i686
> Date and time of compilation         : 07/05/2002
> 17:30:36
> Job starting time (YY/MM/DD HH:MM:SS): 2002/07/18 
> 13:08:16.425
> 
> TOP_________>   105  705 SET ALNFILE  =
> 'alignment.seg.pap'
> 
> TOP_________>   106  706 SET KNOWNS   = '1h9p'
> 
> TOP_________>   107  707 SET SEQUENCE = '1drg'
> 
> 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.seg.pap
> 
> Dynamically allocated memory at         amaxbnd
> [B,kB,MB]:      2560929    2500.907     2.442
> openf5__224_> Open       11  OLD  SEQUENTIAL 
> alignment.seg.pap
> 
> Read the alignment from file       : alignment.seg.pap
> Total number of alignment positions:     0
> 
>   #  Code        #_Res #_Segm PDB_code    Name
> -------------------------------------------------------------------------------
>   1       1h9p       0      1
>   2       1drg       0      1
> TOP_________>   121  107 CHECK_ALIGNMENT
> 
> check_a_343_> >> BEGINNING OF COMMAND
> 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]:      2560929    2500.907     2.442
> Starting time                                         
>   : 2002/07/18  13:08:16.425
> Closing time                                          
>   : 2002/07/18  13:08:17.598
> 
> 
> Frederico Moreno
> 
> 
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