#before running rosetta with this options file, change $WORKSHOP_ROOT to the path of the tutorials directory on your local machine -run:protocol threading #call threading protocol -in:file:fasta /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/2FOXA.fasta #target sequence -in:file:template_pdb /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/1F4PA.pdb #template structure -in:file:fullatom #input will be fullatom -in:file:psipred_ss2 /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/2FOXA.psipred_ss2 #optional: psipred secondary structure -in:file:alignment /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/2FOXA.1F4PA.aln #input alignment -loops:frag_sizes 9 3 1 #sizes of fragments -loops:frag_files /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/aa2FOXA09_05.200_v1_3 /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_input_model/aa2FOXA03_05.200_v1_3 none #fragment files -loops:remodel quick_ccd #use ccd to remodel loops -idealize_after_loop_close #idealize structure after closing loops (structure will have ideal rosetta bond lengths and angles) -loops:extended true #force extended on loops (phi-psi angles set to 180 degrees) independent of loop input file. for rebuilding loops entirely. -loops:build_initial true #precede loop modeling with initial round of removing missing densities and building simple loops -loops:relax fastrelax #fastrelax loops (5 cycles at default) -cm:min_loop_size 4 #minimum size of loops to consider for rebuild -out:nstruct 2 # number of models to build -out:file:silent_struct_type binary #output file type -out:file:silent /mnt/hgfs/ROSETTA/Tutorial/Meiler_Lab/Rosetta_Tutorials/tutorials/modeling/my_output_model/2FOXA_models.out #output file name -out:file:fullatom #output file will be fullatom