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.