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!