rosetta对称性文件(rosetta symmetry file)的产生及应用

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。