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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