Reply To: command lines for rebuilding-and-refinement protocol

[Anonymous]

Here are the command lines for CASP target refinements

aa t020 _ -relax -looprlx -nstruct 10 -farlx -ex1 -ex2 -random_loop -termini -short_range_hb_weight 0.50 -long_range_hb_weight 1.0 -farlx_cycle_ratio 1.0 -idl_no_chain_break -loop_skip_rate 0.3 -loop_file t020.loop_file -vary_omega -s t020_1_id_model_01_idl.pdb -nstruct 100

Vatsan

> Hi,
>
> I’m trying to implement an optimization algorithm in the rebuilding-and-refinement protocol, as described in Qian et. al. 2007 paper. I wonder if I could get a hold of command lines for this protocol. In particular, those for CASP7 predictions. I’m very inexperienced C++ programmer, and I think trying to figure them out myself would lead to a disaster.
>
> In terms of implementing my optimization algorithm, I think I should write functions similar to dfpmin and its versions (if necessary), which are located in minimize.cc. Then I have to figure out where dfpmin gets called when the protocol is used, and then I should modify the necessary files so that the protocol will call my function(s) instead. Does this procedure sound about right?
>
> If there’re any other suggestions or guidelines, please feel free. I’m really need those. Thanks.
>
> Temsiri