I am trying to use loop_modelling. I have small problem on my loop modeling problem. I have missing residues in protein. I gave these missing residues as blank in input pdb. My loop_modelling execution was successful however I did not solve my problem. I am wondering – can Rosetta add missing residues using loop modeling protocol? If so, how can be list of missing residues given in the program (parameter)? If not, could you please tell me any suggestion to put missing residues in the protein during loop modelling?
I’m told the “remodel” application is meant to do this very efficiently, but I’ve never used it.
The simplest way is to use a text editor to add/delete residues manually (using a text editor; garbage coordinates are ok, just make sure all the backbone heavyatoms (C, CA, N, O) are present) and then use the -build_initial option in loop modeling.
There is also a demo in AnchoredDesign/loop_length_changing.
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