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!
Just remove that line. Default is CHAINS_3.5_95_XN.cod in modlib directory, and you don't have to specify it explicitly. .cod file contains PDB codes. Hence, the name 'cod'.
very-short-for-test.cod we used for testing long time ago. You can make your own if you want, containing a subset of CHAINS_3.5_95_XN.cod.
There is more about this in manual ;-) http://salilab.org/modeller/manual/node105.html#20470
> 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.
> SET SEARCH_CHAINS_LIST = 'very-short-for-test.cod' > So I made a file called "very-short-for-test.cod" > Bozidar Yerkovich, PhD Rockefeller University New York, NY, 10021, USA 212-327-7206 firstname.lastname@example.org http://salilab.org/modeller