rosetta对称性文件(rosetta symmetry file)的产生及应用
2018-07-14 16:01 丨o聽乄雨o丨 阅读(708) 评论(0) 编辑 收藏 举报针对对称性PDB 3UKM,使用make_symmdef_file.pl脚本,可以执行产生对称单元及对称文件:
$> $ROSETTA3/src/apps/public/symmetry/make_symmdef_file.pl -m NCS -a A -i B -p 3UKM.pdb > 3UKM.symm
参数意义:
Here we are using symmetry to model an already-symmetric starting protein. This is called non-crystallographic (NCS) mode. We pass the mode (-m NCS), the chain we want to keep (-a A), the chain we want to base the symmetry off of (-i B), and the input PDB (-p 3UKM.pdb).
产生的文件包括:
- 3UKM_INPUT.pdb = chain A
- 3UKM.kin
- 3UKM
_
model_
AB.pdb = model generated to show subunit interactions with the input - 3UKM_symm.pdb = model generated to show the full point group symmetry
- 3UKM.symm = symmetry definition file that you just created
可以用文本编辑器打开文件3UKM.symm,里面记录了对称性信息。
2.使用rosettascripts利用之前产生的3UKM.symm对称性文件,可以重新得到AB两条链对称的PDB结构。
setup_symm.xml
<ROSETTASCRIPTS> <SCOREFXNS> </SCOREFXNS> <TASKOPERATIONS> </TASKOPERATIONS> <FILTERS> </FILTERS> <MOVERS> <SetupForSymmetry name="setup_symm" definition="3UKM.symm" /> </MOVERS> <APPLY_TO_POSE> </APPLY_TO_POSE> <PROTOCOLS> <Add mover_name="setup_symm" /> </PROTOCOLS> </ROSETTASCRIPTS>
命令:
$ rosetta_scripts.linuxgccrelease -parser:protocol setup_symm.xml -s 3UKM_INPUT.pdb -out:prefix setupsymm_
即可产生两条链(AB)的PDB。
作者:丨o聽乄雨o丨
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