Hi John,
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
Best, Bozidar
> 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 bozidar@salilab.org http://salilab.org/modeller