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: modeller_usage-bounces@salilab.org > [mailto:modeller_usage-bounces@salilab.org] On Behalf Of ?? ? > Sent: Friday, September 17, 2004 2:06 PM > To: modeller_usage@salilab.org > 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* > > >