command lines for rebuilding-and-refinement protocol

[Anonymous]

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

[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

[Anonymous]

Thank you so much for the command line. From the command line, I tried to figure out a command to generate a loop file and the ****_1_id_model_01_idl.pdb, but I couldn’t. (>… -loop_file t020.loop_file -vary_omega -s t020_1_id_model_01_idl.pdb …) I tried the ab initio command, but the pdb files were named differently, so I thought you might have used a different command.

Temsiri

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