PROSS程序设计

make_csts.sh input_example.pdb >example.cst

准备文件：refine.flags, refine.xml, example.cst(这个是上一步生成的)
refine.flags：

-use_input_sc
-extrachi_cutoff 5
-in:ignore_unrecognized_res
-chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm
-linmem_ig 10 
-ignore_zero_occupancy false 
-s input_example.pdb # path to structure file 
-out:path:pdb pdbs/ 
-out:path:score scores/ 
-parser:protocol refine.xml 
-parser:script_vars res_to_fix=1A,2A,3A,4A # comma separated list of positions 
-parser:script_vars cst_full_path=example.cst # path to Rosetta CST file of CA atoms

注意：（1）需要手动在此目录下创建两个文件夹(pdbs,scores)
           （2）修改对应的xml，cst以及pdb名称。
refine.xml

接下来输入命令

/home/unbuntu/rosetta2019/main/source/bin/rosetta_scripts.default.linuxgccrelease -database /home/unbuntu/rosetta2019/main/database/ -in:file:s input_example.pdb -parser:protocol refine.xml -parser:script_vars res_to_fix=1A,2A,3A,4A -parser:script_vars pdb_reference=input_example.pdb -parser:script_vars cst_full_path=example.cst -parser:script_vars cst_value=0.4 @refine.flags -overwrite

pdbs文件夹里会生成一个input_example_0001.pdb文件，scores生成score.sc文件

1. path_to_db: path to rosetta database
2. input_pdb: the input structure/model in pdb formant only
3. fix_list: a list (number and chain) of all residues to restrict to minimization separated by commas. Hypothetical Example: 1A,2A,3A,4A
4. cst_file: a file with the input coordinates of all CA atoms in the input_pdb. see example.cst and use make_csts.sh to make one.
5. cst_val: the coordinate constraint weight in the score function. PROSS default is 0.4

-ex1
-ex2
-use_input_sc
-extrachi_cutoff 5
-ignore_unrecognized_res
-use_occurrence_data
#-corrections::correct
#-corrections::score:no_his_his_pairE
-chemical:exclude_patches LowerDNA  UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated  tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated  lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm
#-output_virtual
-linmem_ig 10
-ignore_zero_occupancy false

#-out:path:pdb pdbs/
#-out:path:score scores/
-restore_talaris_behavior true

结束会生成input_example_0001_0001.pdb和score.sc文件

/home/unbuntu/rosetta2019/main/source/bin/rosetta_scripts.default.linuxgccrelease -database /home/unbuntu/rosetta2019/main/database/ -in:file:s pdbs/input_example_0001.pdb -parser:protocol design.xml -parser:script_vars in_resfile=resfiles -parser:script_vars res_to_fix=1A,2A,3A,4A -parser:script_vars pdb_reference=pdbs/input_example_0001.pdb -parser:script_vars cst_full_path=example.cst -parser:script_vars cst_value=0.4 -parser:script_vars pssm_full_path=example.pssm @flags -overwrite

其中relax_mover=min_all删除，一直报错：没有min_all换了whole_min也报错

-use_input_sc 
-extrachi_cutoff 5 
-ignore_unrecognized_res
-chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm
-linmem_ig 10 
-ignore_zero_occupancy false 
-s # path to structure file 
-out:path:pdb filterpdbs 
-out:path:score filterscores
-parser:protocol filterscan.xml 
-parser:script_vars current_res=1-73A # a position to mutational ddG for 
-parser:script_vars res_to_fix=1A,2A,3A,4A # comma separated list of positions 
-parser:script_vars cst_full_path=example.cst # path to Rosetta CST file of CA atoms 
-parser:script_vars pssm_full_path=example.pssm # path to pssm file

/home/unbuntu/rosetta2019/main/source/bin/rosetta_scripts.default.linuxgccrelease -database /home/unbuntu/rosetta2019/main/database/ -in:file:s input_example_0001.pdb -parser:protocol filterscan.xml -parser:script_vars res_to_fix=1A,2A,3A,4A -parser:script_vars pdb_reference=input_example_0001.pdb -parser:script_vars res_to_restrict=10A,11A,12A,13A,14A,15A,16A,17A,18A -parser:script_vars cst_full_path=example.cst -parser:script_vars cst_value=0.4 -parser:script_vars pssm_full_path=example.pssm -parser:script_vars scores_path=scores/ -parser:script_vars resfiles_path=resfiles/ @flags -parser:script_vars current_res=${i} -overwrite

创建两个文件夹filterscanpdbs和filterscanscores，生成的文件会放入对应文件夹。
运行命令：

/home/unbuntu/rosetta2019/main/source/bin/rosetta_scripts.default.linuxgccrelease -database /home/unbuntu/rosetta2019/main/database/ -in:file:s pdbs/input_example_0001.pdb -parser:protocol filterscan.xml -parser:script_vars res_to_fix=1A,2A,3A,4A -parser:script_vars pdb_reference=pdbs/input_example_0001.pdb -parser:script_vars res_to_restrict=10A,11A,12A,13A,14A,15A,16A,17A,18A -parser:script_vars cst_full_path=example.cst -parser:script_vars cst_value=0.4 -parser:script_vars pssm_full_path=example.pssm -parser:script_vars scores_path=scores/ -parser:script_vars resfiles_path=resfiles/ @filterscan.flags -parser:script_vars current_res=1-73A -overwrite

其中current_res=1-73A参数，不确定是不是填序列长度。
current_res=${i}
i - the residue number (this script is for a single residue. you need to run it for every residue)