rosetta-fixbb
purpose：
use fixbb application to invoke the Rosetta packer to optimize the side-chain conformations of an input structure.
basic command：
fixbb.static.linuxgccrelease -in:file:s 1l2y.pdb -in:file:fullatom -resfile resfile.txt -nstruct 5 >log.txt eplain:
-in:file:s 1l2y.pdb : the input PDB file
-in:file:fullatom: the input file is a full-atom respresentation (as opposed to a centroid-only model)--（全原子模型区别于质心模型）
-resfile resfile.txt : controlling the packer（rosetta中的文件，用于控制packer）.
-nstruct 5: tells Rosetta to repeat the protocol five times, producing five independent outputs. （重复5次，得到5个结构，但由于rosetta使用随机算法，所以实际数目需要提升）
resfile:
NATAA
start```
input：
1l2y.pdboutput：
1l2y_0001.pdb
1l2y_0002.pdb
1l2y_0003.pdb
1l2y_0004.pdb
1l2y_0005.pdb
log.txt
score.scstep：
（1）pymol->open 1l2y.pdb(observe)
（2）output:
score.sc
SEQUENCE:
SCORE: total_score dslf_fa13 fa_atr fa_dun fa_elec fa_intra_rep fa_intra_sol_xover4 fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb lk_ball_wtd omega p_aa_pp pro_close rama_prepro ref yhh_planarity description
SCORE: -13.104 0.000 -75.943 18.637 -17.270 0.173 3.270 12.601 57.560 -1.336 -1.005 0.000 -6.434 -2.802 2.415 -6.345 3.741 1.959 -2.324 0.000 1l2y_0001
SCORE: -13.104 0.000 -75.943 18.637 -17.270 0.173 3.270 12.601 57.560 -1.336 -1.005 0.000 -6.434 -2.802 2.415 -6.345 3.741 1.959 -2.324 0.000 1l2y_0002
SCORE: -13.104 0.000 -75.943 18.637 -17.270 0.173 3.270 12.601 57.560 -1.336 -1.005 0.000 -6.434 -2.802 2.415 -6.345 3.741 1.959 -2.324 0.000 1l2y_0003
SCORE: -13.104 0.000 -75.943 18.637 -17.270 0.173 3.270 12.601 57.560 -1.336 -1.005 0.000 -6.434 -2.802 2.415 -6.345 3.741 1.959 -2.324 0.000 1l2y_0004
SCORE: -13.104 0.000 -75.943 18.637 -17.270 0.173 3.270 12.601 57.560 -1.336 -1.005 0.000 -6.434 -2.802 2.415 -6.345 3.741 1.959 -2.324 0.000 1l2y_0005pdb:
better command：
fixbb.static.linuxgccrelease -in:file:s 1l2y.pdb -in:file:fullatom -resfile resfile.txt -nstruct 1 -ex1 -ex2 -ex3 -ex4 -extrachi_cutoff 0 -out:prefix run2_ -out:file:scorefile run2.sc >log2.txt``` "-ex1", "-ex2", "-ex3", and "-ex4" :activate extra rotamers for the first, second, third, and fourth side-chain chi angles(控制侧链旋转角度).
-extrachi_cutoff: flag determines the number of residue neighbours (nearby residues) that a resiude must have in order to receive the additional rotamers（如果你想使所有的残基侧链进行旋转，将它设置为0）.
-out:prefix run2_ :write PDB files with the prefix "run2_" in the filename(以run2_作为前缀)
-out:file:scorefile run2.sc：directs the final scores to a new file（输出得分文件）
run2.sc
SEQUENCE:
SCORE: total_score dslf_fa13 fa_atr fa_dun fa_elec fa_intra_rep fa_intra_sol_xover4 fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb lk_ball_wtd omega p_aa_pp pro_close rama_prepro ref yhh_planarity description
SCORE: -21.078 0.000 -80.039 20.857 -24.261 0.176 3.379 11.104 60.743 -0.800 -1.005 -1.813 -6.434 -2.428 2.415 -6.345 3.741 1.959 -2.324 0.000 run2_1l2y_0001
SCORE: -21.078 0.000 -80.039 20.857 -24.261 0.176 3.379 11.104 60.743 -0.800 -1.005 -1.813 -6.434 -2.428 2.415 -6.345 3.741 1.959 -2.324 0.000 run2_1l2y_0002
SCORE: -20.799 0.000 -77.560 19.762 -19.161 0.165 3.106 9.948 55.829 -0.800 -1.005 -0.917 -6.434 -3.178 2.415 -6.345 3.741 1.959 -2.324 0.000 run2_1l2y_0003
SCORE: -21.078 0.000 -80.039 20.857 -24.261 0.176 3.379 11.104 60.743 -0.800 -1.005 -1.813 -6.434 -2.428 2.415 -6.345 3.741 1.959 -2.324 0.000 run2_1l2y_0004
SCORE: -20.798 0.000 -77.364 19.993 -18.947 0.163 3.085 9.608 55.796 -0.800 -1.005 -1.031 -6.434 -3.307 2.415 -6.345 3.741 1.959 -2.324 0.000 run2_1l2y_0005reference:
http://www.ccp14.ac.uk/ccp/web-mirrors/garlic/garlic/commands/dihedrals.html