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Attempting to run the first tutorial



Dear MODELLER users,

I installed modeller onto my computer.  It looks as
though I am having problems getting the program to
run properly.  

I am running the program using bash instead of csh. 
In the installation, I accepted all defaults except
for the program location.  The program is located in
a directory named /modeller.  The program then can
be found in /modeller/bin/mod6v2.  

Running the tutorial files included in the
installation seem to work.  I think that
model-default.top is working properly.  The problem
comes when I attempt to run the tutorials from
http://salilab.org/modeller/user_manual.shtml.  

The first tutorial generates this message:

$ mod6v2 seq_search.top
/modeller/bin/mod6v2: line 38:  1360
Killed                  $NICE ${EXECUTABLE} $STEERF
>$LOGF

The seq_search.top file looks like this:

SET SEARCH_RANDOMIZATIONS = 100
SEQUENCE_SEARCH FILE = 'TvLDH.ali', ALIGN_CODES =
'TvLDH', DATA_FILE =ON

I read that going into emacs and saving it may clear
up the problem, but it did not.

The output file seq_search.log starts off well I
think.  But I don' t know if the end is correct.  It
aligns over 800 sequences.  From the .top file, I
thought it would only align 100 sequences.


Here is the start:


                         MODELLER 6v2, 17 Feb 2002

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF
SPATIAL RESTRAINTS


                     Copyright(c) 1989-2002 Andrej Sali
                            All Rights Reserved

                            Written by A. Sali
          with help from A. Fiser, R. Sanchez, M.A.
Marti-Renom,
                   B. Jerkovic, A. Badretdinov, F. Melo,
                       J.P. Overington & E. Feyfant
                   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, Linux
dhcppc2 2.4.18-14 i686
Date and time of compilation         : 07/16/2002
11:42:16
Job starting time (YY/MM/DD HH:MM:SS): 2003/07/28 
22:20:50.755



seqsearc_>    1  TvLDH  1xnb    335  185   63  
18.81   34.05  117083.50

 _aln.pos         10        20        30       
40        50        60
TvLDH    
MSEAAHVLITGAAGQIGYILSHWI-ASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGF
1xnb     
ASTDYWQNWT-DGG--G-IVNA-VNGSG---GN---Y----SV----N-WSN-T-G--N--F--VVG-
 _consrvd  *       *   *  * *       **   *   
*          *     *       *    *


 _aln.p   70        80        90       100      
110       120       130
TvLDH    
VATTDPKAAFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTN
1xnb     
------KG-WT----T---GS-PF-----RT--I--N---Y-NAG--V--WA-PN------GN-GY--
 _consrvd       *             * *      *   *  *    
* *     ** *       **


 _aln.pos  140       150       160       170      
180       190       200
TvLDH    
CEIAMLHAKNLKPENFSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEG
1xnb     
--LT-LYGWT-R----SPL--IE----YY-V-----VD--S------WGTY--R--P--T-GTY-K-G
 _consrvd      *          * *        ** *    
**         **          *  *  * *


 _aln.pos    210       220       230       240      
250       260       270
TvLDH    
KTQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPV
1xnb     
-TVKS-DGGTYD-IYTT--TRYN--APSI-D--G--DR-T-T-FT-QY---W---SV-RQ--S-K--R
 _consrvd  * *  *    *    *        *  *    *      
*    *    *          *


 _aln.pos      280       290       300      
310       320       330
TvLDH    
PEGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKV-NDWLREKLDFTEKDLFHEKEIALNHLAQGG
1xnb     
PTGSN-A-T--ITFT-N-HVNA-WKSH---GMNLGSNWAYQVMA-TE-G-YQSSG-SSN-VTVW-
 _consrvd * *          *     *    * *   *     
*       **           *


It continues on until this point.


 _aln.pos      280       290       300      
310       320       330
TvLDH    
EGNPYGIKPGVVFSFPCNVDKEGKIHVVEGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG
1ayaA    
Q---Y-------Y-----M--E-H-H---G-Q----LKEK-N--G-DVI-ELKYPLN------
 _consrvd     *                *   *   *      *
**      *   *    **


seqsearc_>  897  TvLDH  1az4A   335  187   77  
22.99   41.18  123537.50

 _aln.pos         10        20        30       
40        50        60
TvLDH    
MSEAAHVLITGAAGQI-GYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGF
1az4A    
-SLRSD-LIN-ALYDVCG-IIS---A--E--G-K-IY------P-----LSTI-FEL----FS-RP-I
 _consrvd  *     **  *     * * *   *  *  *    *     
*     *     **    *

 (Fundamental)--L32747--Bot-----------------

This leads me to think that it went over its 100
alignment limit and ended up timing out.  I'm not
sure how many hours this took.  I believe it was
over four hours.  As you can see, the output file is
32 747 lines long.

Here is what the install program included with the
.bashrc file.  I've removed the key in case you
don't want it displayed in the forum.

### begin
MODELLER6v2##################################################

MODINSTALL6v2=/modeller
EXECUTABLE_TYPE6v2=i386-absoft
LIBS_LIB6v2=$MODINSTALL6v2/modlib/libs.lib
KEY_MODELLER6v2=xxx
mod=mod6v2
export MODINSTALL6v2 EXECUTABLE_TYPE6v2 LIBS_LIB6v2
KEY_MODELLER6v2 mod
PATH=$PATH:$MODINSTALL6v2/bin
ulimit -S -s unlimited

### end
MODELLER6v2####################################################

My computer has a 500 mb swap file.  I don't know if
that is adequate or if it is not enough for this
program.  Perhaps I am missing another setting of
some sort.  

Your help would be much appreciated.  I've been
trying to get the program to work for over a week so
I'm perplexed.

Thanks 

Andrew L
University of Idaho
;-)