Hi friends:
 
    After the installation of modeller in my PC I tried to follow a similar example like those are illustrated in the WEB page.
I prepared a file liki this:
 
XUFF11.ali
 
>P1;XUFF11
sequence:XUFF11:::::::0.00: 0.00
MVDFYYLPGSSPCRSVIMTAKAVGVELNKKLLNLQAGEHLKPEFLKINPQHTIPTLVDNGFALWESRAIQVYLVEKYGKTDSLY
PKCPKKRAVINQRLYFDMGTLYQSFANYYYPQVFAKAPADPEAFKKIEAAFEFLNTFLEGQDYAAGDSLTVADIALVATVSTFE
VAKFEISKYANVNRWYENAKKVTPGWEENWAGCLEFKKYFE*  
and a script file like this:
 
SET SEARCH_RANDOMIZATIONS = 100
SET FILE = 'XUFF11.ali'
READ_SEQUENCE_DB
SEQUENCE_SEARCH ALIGN_CODES = 'XUF11', DATA_FILE = ON
The program worked and after an hour the process finished. The log file showed this information in the last lines:
 
ddgrp__223E> Array too small. Increase  MAXSEQ
              current maximum, current need:       80      115
addgrp__223E> Array too small. Increase  MAXSEQ
              current maximum, current need:       80       87
addgrp__223E> Array too small. Increase  MAXSEQ
              current maximum, current need:       80       83
addgrp__223E> Array too small. Increase  MAXSEQ
              current maximum, current need:       80       84
Then I tried to run the following script:
 
READ_MODEL FILE = '1jlv.pdb'
SEQUENCE_TO_ALI ALIGN_CODES = '1jlv'
READ_ALIGNMENT FILE = 'XUFF11.ali', ALIGN_CODES = 'XUFF11', ADD_SEQUENCE = ON
ALIGN2D
WRITE_ALIGNMENT FILE='XUFF11-1jlv.ali', ALIGNMENT_FORMAT = 'PIR'
having the 1jlv.pdb file in the same directory that the script files and then i received the next message in the console:
 
C:\bioinfo\Modeller7v7\examples\commands>mod7v7 align2d.top
forrtl: severe (170): Program Exception - stack overflow
Image              PC        Routine            Line        Source
mod7v7.exe         006045E6  Unknown               Unknown  Unknown
mod7v7.exe         004D1CAF  Unknown               Unknown  Unknown
mod7v7.exe         004066D8  Unknown               Unknown  Unknown
mod7v7.exe         0040F5BB  Unknown               Unknown  Unknown
mod7v7.exe         006A564B  Unknown               Unknown  Unknown
mod7v7.exe         006EDB39  Unknown               Unknown  Unknown
mod7v7.exe         006DC824  Unknown               Unknown  Unknown
kernel32.dll       7C816D4F  Unknown               Unknown  Unknown
 
and the content of the log file was:
 

                         MODELLER 7v7, Sep 12, 2004 09:15pm
 
     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
 
.....

Kind, OS, HostName, Kernel, Processor: 4, WinXP build  2600 Service Pack 2, HPPAVILION, uni, x86 Family  15 Model  2 Stepping  9
Date and time of compilation         : 09/13/2004 17:17:22
Job starting time (YY/MM/DD HH:MM:SS): 2004/11/16  22:56:43.406
 
 
My queestion is What happened?
 
 
Alfonso Mendez Tenorio
Escuela Nacional de Ciencias Biológicas
Mexico city.
 
 
 



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