Usage

["Lewis, John" <>]

Very new here any help would be great!  When I get this figured out I 
am going to do some documentation for dummies on this.

When I run 'mod sequence_search' I get an error "fullfn__230E> File not 
found:  very-short-for-test.cod"  What is the .cod file?  Here is a 
copy of my script.

# Example for: SEQUENCE_SEARCH

# This will search the MODELLER database of representative protein 
chains
# for chains similar to the specified sequence.

SET OUTPUT_CONTROL = 1 1 1 1 1
SET SEARCH_RANDOMIZATIONS = 20 # should use 100 in real life;
SET GAP_PENALTIES_1D = -800 -400
SET SEARCH_CHAINS_LIST = 'very-short-for-test.cod'
SEQUENCE_SEARCH FILE = 'P450.ali', ALIGN_CODES = '1nbt'
MALIGN
WRITE_ALIGNMENT FILE = 'toxin-search.pap', ALIGNMENT_FORMAT = 'PAP'


So I made a file called "very-short-for-test.cod"

I then get an error in this log:

Date and time of compilation         : 07/19/2002 11:38:41
Job starting time (YY/MM/DD HH:MM:SS): 2002/10/15  14:49:24.094


Dynamically allocated memory at         amaxseq [B,kB,MB]:      2200483 
   2148.909     2.099
TOP_________>     2    2 SET SEARCH_RANDOMIZATIONS = 20

TOP_________>     3    3 SET GAP_PENALTIES_1D = -800 -400

TOP_________>     4    4 SET SEARCH_CHAINS_LIST = 
'very-short-for-test.cod'

TOP_________>     5    5 SEQUENCE_SEARCH FILE = 'P450.ali', ALIGN_CODES 
= '1nbt'

openf5__224_> Open       11  OLD  SEQUENTIAL  very-short-for-test.cod
amaxchn_215E> Dynamic memory allocation failed.
              Routine, variable, status:  iseqdb         3
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:      2200483 
   2148.909     2.099
Starting time                                            : 2002/10/15  
14:49:24.094
Closing time                                             : 2002/10/15  
14:49:28.614
Total CPU time [seconds]                                 :       4.36

thank you for any help!