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Other STACK PROBLEMS and Re: [modeller_usage] Modeller 7v7 Stack problems, tried EVERYTHING!!!!

Dear all Modeller user,

   I  follow by so near this question and answers because I have the same error message.

    I do the download of "Updated Windows binary"   and I have the same problem of STACK OVERFLOW.

    I do my example (top scripts) exactly as the example from Modeller basic tutorial  avec my data, of course.


    My sequence file is :

>P1;rpb3
sequence:rpb3:::::::0.00: 0.00
MVALTVEELTPEHIRFTLSNTTVGYANALRRILISEVPTIAIDMVEIERNNTVLPDEVLA
HRLGLIPIYSKRELKYKEECSCSGFCSECSVVFEIDVVHTDDTLRTVSTRDIVCDEEDVI
IKSGPVITKLARDQGLKARCIGRKGVGKTHAKWSPVSAISFEYDKDNVRRETNYWFEESI
EEEWPGVRQGEANLMQKIDKIHMCVEVVEGGAGPLAVVLEGLRILKEKVATLSSAAETMD
*
   

     My script file is:

# Example to ALIGN RPB3 with the Template
#
# the template is 1i50C (pdb1i50.ent at C:\Program Files\Modeller7v7\examples\Testes\atom_files)
#
SET OUTPUT_CONTROL = 1 1 1 1 0

# directory with input atom files
SET ATOM_FILES_DIRECTORY = './:../atom_files'

READ_MODEL FILE = 'pdb1i50.ent'

SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1i50C', ATOM_FILES=ALIGN_CODES , ADD_SEQUENCE = on

READ_ALIGNMENT FILE = 'rpb3.ali', ALIGN_CODES = ALIGN_CODES 'rpb3'

ALIGN2D

WRITE_ALIGNMENT FILE='rpb3-1i50.ali', ALIGNMENT_FORMAT = 'PIR'
WRITE_ALIGNMENT FILE='rpb3-1i50.pap', ALIGNMENT_FORMAT = 'PAP'


    I find an information at the FAQ messages that there are a Modeller's Variable called "MAXRES".  I follow this suggestion from an modeller user: SET MAXRES=5000, and I did not get sucessful!!!  but if I uses this ligne above:

        SET MAXRES  = 50000000

   I have no 'stack overflow' error message but I have '_E> modeller error message (se the log file above)

   Can you give some help ?

   Many thanks.



My LOG file is :


                         MODELLER 7v7, Sep 12, 2004 09:15pm

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

                                                                  
                     Copyright(c) 1989-2004 Andrej Sali           
                            All Rights Reserved                   
                                                                  
                             Written by A. Sali                   
                               with help from                     
           B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
                     N. Eswar, F. Alber, B. Oliva, A. Fiser,      
                    R. Sanchez, B. Yerkovich, A. Badretdinov,     
                      F. Melo, J.P. Overington, E. Feyfant        
                 University of California, San Francisco, USA     
                    Rockefeller University, New York, USA         
                      Harvard University, Cambridge, USA          
                   Imperial Cancer Research Fund, London, UK      
              Birkbeck College, University of London, London, UK  


Kind, OS, HostName, Kernel, Processor: 4, WinXP build  2600 Service Pack 2, SANTOS, 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): 2005/01/24  12:06:44.218

TOP_________>     2    2 SET ATOM_FILES_DIRECTORY = './:../atom_files'
 
TOP_________>     3    3 READ_MODEL FILE = 'pdb1i50.ent'
 
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\pdb1i50.ent
openf5__224_> Open       11  OLD  SEQUENTIAL  ../atom_files\pdb1i50.ent
rdatm___297_> Segments, residues, atoms:       10     3558    28279
rdatm___298_> Segment:        1     2 A  1450 A    11154
rdatm___298_> Segment:        2    18 B  1224 B     8711
rdatm___298_> Segment:        3     3 C   268 C     2095
rdatm___298_> Segment:        4     1 E   215 E     1760
rdatm___298_> Segment:        5    72 F   155 F      679
rdatm___298_> Segment:        6     2 H   146 H     1068
rdatm___298_> Segment:        7     1 I   122 I      997
rdatm___298_> Segment:        8     1 J    65 J      532
rdatm___298_> Segment:        9     1 K   114 K      919
rdatm___298_> Segment:       10    25 L    70 L      364
TOP_________>     4    4 SEQUENCE_TO_ALI ALIGN_CODES = ALIGN_CODES '1i50C', ATOM_F;
                      ILES =ALIGN_CODES , ADD_SEQUENCE = ON
 
TOP_________>     5    5 SET MAXRES  = 50000000
 
TOP_________>     6    6 READ_ALIGNMENT FILE = 'rpb3.ali', ALIGN_CODES = ALIGN_COD;
                      ES 'rpb3'
 
openf5__224_> Open       20  OLD  SEQUENTIAL  rpb3.ali
amaxres_215E> Dynamic memory allocation failed.
              Routine, variable, status:  irestypn2         2
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:   2102291815 2053019.375  2004.902
Starting time                                            : 2005/01/24  12:06:44.218
Closing time                                             : 2005/01/24  12:08:38.125
Total CPU time [seconds]                                 :      37.66


Tom Petty wrote:
I have a windows XP SP2 IBM laptop with plenty of memory (512MB RAM) ....

C:\Program Files\Modeller7v7\examples\tutorial-model>mod7v7 Toms-Initial
forrtl: severe (170): Program Exception - stack overflow

This means that Modeller has exceeded the stack space limit. This a constant, set when the Modeller binary was linked, so it won't help if you add more memory to your machine.
...

Alternatively, you can download just such a 'fixed' binary from the Modeller downloads page:
http://salilab.org/modeller/download_installation.html
(The link is right at the bottom: "Updated Windows binary".)
Use this binary to replace the existing mod7v7.exe file in your Modeller installation (by default it should be in
C:\Program Files\modeller7v7\bin), and all should be well.

If these problems persist, let me know.

	Ben Webb, Modeller Caretaker

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