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Re: Alignment problem
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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