在设计蛋白质之前我想对一个蛋白质结构进行最简单的relaxxml是否要包含以下语句FastRelax name=example1 relaxscript=default如果是的请帮我写出这个脚本
是的,要包含该语句。以下是一个简单的默认relax脚本示例:
<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="scorefxn" />
</SCOREFXNS>
<RESIDUE_SELECTORS>
<All name="all" />
</RESIDUE_SELECTORS>
<TASKOPERATIONS>
<ResidueTypeSetSelector name="no_proline" >
<ResidueTypes>
<ResidueType name="ALA" />
<ResidueType name="ARG" />
<ResidueType name="ASN" />
<ResidueType name="ASP" />
<ResidueType name="CYS" />
<ResidueType name="GLN" />
<ResidueType name="GLU" />
<ResidueType name="GLY" />
<ResidueType name="HIS" />
<ResidueType name="ILE" />
<ResidueType name="LEU" />
<ResidueType name="LYS" />
<ResidueType name="MET" />
<ResidueType name="PHE" />
<ResidueType name="SER" />
<ResidueType name="THR" />
<ResidueType name="TRP" />
<ResidueType name="TYR" />
<ResidueType name="VAL" />
</ResidueTypes>
</ResidueTypeSetSelector>
<OperateOnResidueSubset name="no_proline_task" selector="no_proline">
<PreventRepackingRLT />
<PreventDesign />
</OperateOnResidueSubset>
</TASKOPERATIONS>
<FILTERS>
<RMSD name="rmsd" reference_name="native" />
</FILTERS>
<MOVERS>
<FastRelax name="relax" scorefxn="scorefxn" task_operations="no_proline_task" />
</MOVERS>
<PROTOCOLS>
<Add mover_name="relax" />
<Add filter_name="rmsd" />
</PROTOCOLS>
</ROSETTASCRIPTS>
该脚本使用默认的score function(scorefxn),选择所有氨基酸残基(all),并对所有非脯氨酸残基执行禁止重组和禁止设计的任务操作。然后使用FastRelax进行relax,并使用RMSD filter评估结果
原文地址: https://www.cveoy.top/t/topic/cpXs 著作权归作者所有。请勿转载和采集!