{\rtf1\ansi\ansicpg1252\cocoartf2513 \cocoatextscaling0\cocoaplatform0{\fonttbl\f0\fswiss\fcharset0 Helvetica;} {\colortbl;\red255\green255\blue255;} {\*\expandedcolortbl;;} \margl1440\margr1440\vieww10800\viewh8400\viewkind0 \pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\tx5040\tx5760\tx6480\tx7200\tx7920\tx8640\pardirnatural\partightenfactor0 \f0\fs24 \cf0 -run:protocol threading # run the rosetta threading, loopbuilding, and refinement protocol\ -in:file:alignment 3.1_4f5b.aln # path to alignment file\ -cm:aln_format general # format of alignment file\ -frag3 aat000_03_05.200_v1_3.txt # path in 9mer fragment file\ -frag9 aat000_09_05.200_v1_3.txt # path to 3mer fragment file\ -in:file:fasta t000_.fasta # path to target fasta file\ -in:file:fullatom # we have fullatom format for the input template\ -loops:frag_sizes 9 3 1 # which size fragments are you using?\ -loops:frag_files aat000_09_05.200_v1_3.txt aat000_03_05.200_v1_3.txt none # paths to 9mer file, 3mer file, and say "none" for the 1mer file\ -in:file:psipred_ss2 t000_.psipred_ss2.txt # path to psipred secondary structure prediction file\ -in:file:fullatom \ -out:nstruct 1 # number of structures you want to build. Should build at least 1000, but 10,000 would be better\ -in:file:template_pdb 4f5b_no_ligand_A.pdb # path to template pdb\ -loops:extended # Force extended on loops, independent of loop input file\ -loops:build_initial # Precede loop-modeling with an initial round of just removing the missing densities and building simple loops\ -loops:remodel quick_ccd # closing loops by quick_ccd\ -loops:refine refine_ccd # small movements to remodel loop\ -random_grow_loops_by 4 # randomly grow loops by up to this number of residues on either side.\ -select_best_loop_from 1 # Keep building loops until N and choose best (by score)\ -out:file:fullatom # output in fullatom mode\ -out:output\ -out:pdb\ -out:file:silent_struct_type binary # output the silent file in binary format\ -run:constant_seed # Use a constant seed (1111111 unless specified)\ -run:jran 1111111 # this is good for testing since you should always get the same result\ -overwrite # overwrite any already-existing results having the same name\ \ }