I would like to model inserted domains of unknown structure and large loops. I have been looking at the several loop modeling options and have a few queries
1) Most basically, is use of the loop protocols the way to go? The advantage is the use of the environment from the 'host' domain, but are any of the protocols capable of ab initio modeling of large domain insertions (50-100 residues)? The inserted domain could be modeled alone, but that modeling loses the context information from the host domain.
2) After some work, I have made got the template structures read in, albeit with this warning
WARNING:: end of pdb file reached: angle, secstruct, & res info not found
I then see this error
increase max_loop_depth in loops_ns.cc
I have tried editing loops_ns.cc, but with no effect. Does this need recompilation? Is there an alternative workaround? If not, what is the minimum unit that could be recompiled and what would be the command for that?
3) While making the loop file, the script looked for but didn't find
Checking again, this file isn't in rosetta_fragments-2.3.0.tgz. Should it be?
I could get the loops by substituting with vall_cst_coord.dat.2001-02-02. Will performance be much degraded by using this older, smaller file instead?
Thanks very much in advance for your help