RE: [modeller_usage] Problem with alignment file

["Schweikardt, Thorsten" <>]

Hi Charles (?),

check your input pdb file, find out if all aminoacids in your alignment
are present in 
your pdb file. You should also specify the chain ID in your alignment,
your
chain of interest is called "E":

structureX:1stc:15:E:350:E::::

do you really have a space in front of  "P1;1stc"? Maybe that's also a
problem, 
but I do not know how your system handles this (you are using a Mac,
right?)

Best wishes,

Thorsten Schweikardt
Molecular Biophysics
University of Mainz, 
Germany




> -----Original Message-----
> From:  
> [">mailto:] On Behalf Of ?? ?
> Sent: Friday, September 17, 2004 2:06 PM
> To: 
> Subject: [modeller_usage] Problem with alignment file
> 
> 
> Please help me.  I cannot figure out  this error.
> 
> --
> 
>                           MODELLER 7v7, Sep 12, 2004 09:15pm
> 
> Kind, OS, HostName, Kernel, Processor: 4, Darwin  7.5.0 Power 
> Macintosh
> Date and time of compilation         : 09/14/2004 09:31:49
> Job starting time (YY/MM/DD HH:MM:SS): 2004/09/17  20:55:55.058
> 
> TOP_________>   109  749 SET ALNFILE  = 'align.txt'
> 
> TOP_________>   110  750 SET KNOWNS   = '1stc'
> 
> TOP_________>   111  751 SET SEQUENCE = 'pkcAcat'
> 
> TOP_________>   112  752 SET ATOM_FILES_DIRECTORY = './'
> 
> TOP_________>   113  753 SET STARTING_MODEL = 1
> 
> TOP_________>   114  754 SET ENDING_MODEL  = 1
> 
> TOP_________>   115  755 SET HETATM_IO = ON
> 
> TOP_________>   116  756 CALL ROUTINE = 'model'
> 
> TOP_________>   117  419 CALL ROUTINE = 'getnames'
> 
> TOP_________>   118  534 STRING_IF STRING_ARGUMENTS = MODEL 
> 'undefined', OPERATION;
>                         = 'EQ', THEN =     'STRING_OPERATE 
> OPERATION = 
> CONCATENA;
>                        TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = 
> MODEL'
> 
> TOP_________>   119  535 STRING_IF STRING_ARGUMENTS = CSRFILE 
> 'undefined', OPERATI;
>                        ON = 'EQ', THEN =     'STRING_OPERATE 
> OPERATION = 
> CONCATE;
>                        NATE, STRING_ARGUMENTS = SEQUENCE 
> .rsr,  RESULT = 
> CSRFILE;
>                        '
> 
> TOP_________>   120  536 STRING_OPERATE OPERATION = 
> 'CONCATENATE',      
>            ;
>                           STRING_ARGUMENTS = SEQUENCE '.sch', 
>  RESULT = 
> SCHFILE
> 
> TOP_________>   121  537 STRING_OPERATE OPERATION = 
> 'CONCATENATE',      
>            ;
>                          STRING_ARGUMENTS = SEQUENCE '.mat',  
> RESULT = 
> MATRIX_FI;
>                        LE
> 
> TOP_________>   122  538 SET ROOT_NAME = SEQUENCE
> 
> TOP_________>   123  539 RETURN
> 
> TOP_________>   124  420 CALL ROUTINE = 'homcsr'
> 
> TOP_________>   125  112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = 
> KNOWNS SEQUE;
>                        NCE
> 
> 
> Dynamically allocated memory at         amaxseq [B,kB,MB]:    
>     84067 
>       82.097     0.080
> openf5__224_> Open       20  OLD  SEQUENTIAL  align.txt
> rdpir___270E> Error reading/processing file:  align.txt
> recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1
> 
> Dynamically allocated memory at          finish [B,kB,MB]:    
>     84067 
>       82.097     0.080
> Starting time                                            : 
> 2004/09/17  
> 20:55:55.058
> Closing time                                             : 
> 2004/09/17  
> 20:55:57.131
> Total CPU time [seconds]                                 :       1.88
> 
> --
>  >P1;1stc
> structureX:1stc:15::350:::::
> GNAAAAKKGSEQESVKEFLAKAKEDFLKKWESPAQNTAHLD-----QFERIKTLGTGSFG
> RVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVN-FPFLVKLEFSFKDNS
> NLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTFEYLHSLDLIYRDLKPENLLI
> DQQGYIQVTDFGFAKRVKGR---TWTLCGTPEYLAPEIILSKGYNKAVDWWALGVLIYEM
> AAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDI
> KNHKWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEE-------EIRVSINEKCG
> KEFSEF*
> 
> 
>  >P1;pkcAcat
> sequence:pkcAcat:1::336:::::
> EGDEEGNMELRQKFEKAKLGPAGNKVISPSEDRKQPSNNLDRVKLTDFNFLMVLGKGSFG
> KVMLADRKGTEELYAIKILKKDVVIQDDDVECTMVEKRVLALLDKPPFLTQLHSCFQTVD
> RLYFVMEYVNGGDLMYHIQQVGKFKEPQAVFYAAEISIGLFFLHKRGIIYRDLKLDNVML
> DSEGHIKIADFGMCKEHMMDGVTTRTFCGTPDYIAPEIIAYQPYGKSVDWWAYGVLLYEM
> LAGQPPFDGEDEDELFQSIMEHNVSYPKSLSKEAVSICKGLMTKHPAKRLGCGPEGERDV
> REHAFFRRIDWEKLENREIQPPFKPKVCGKG-AENFDKFFTRGQPVLTPPDQLVIANIDQ
> SDFEGF*
> 
> 
>