Reply To: Can Rosetta Antibody build a good model for a new sequence??

[Anonymous]

Maybe you have launched only the preparatory script:

perl -P $ROSETTA_ANTIBODY_PATH/scripts/ram_buildloop_wrapper4.pl pdb1xyz_chothia.pdb bit ram ram 1 1 1 1 1 0 0 1 1 0 0 0 0 FR02 2 1 3 2000 2000 3 0 query_l.fasta query_h.fasta

after that you’ll have to move to the ./build directory and then launch the ./1xyz_build_loops.bash script that will start the actual modeling (by default it will produce 2000 models, in some days of calculations).

However i would like to point out that the scripts coming with Rosetta2.3 (antibody in particular) are full of funny local paths, you have to found, and replace.
I don’t uderstant why : to launch any script you need to have all the “path.txt” or “rampath.txt” stuff, and then some part of the script doesn’t use the path given by user, making the debugging quite tedious.

I’ve also found a problem with the precompiled version of blast coming with my distribution (Ubuntu 11.04):
blastall -p blastp versus the fragments database does give a “No Hit Found” even if (checking by hand) the target sequence was present!!
Resolved by recompiling ncbi-blast.
But it’s still not clear to me, why i have to download the full non-redundant blast database in order to model an antibody, given the presence of antibody sequences database.

However I’ve found that when the fragment alignment doesn’t find any match for H3 in the fragment database it exit with error… it isn’t possible to try something else?