如何快速修正pdb中突变后的残基

一：利用pdbset生成pdb对应的seq。（命令如下）
pdbset xyzin 2010-05-HOME-pro_refine_8.pdb << eof-1
sequence SINGLE
eof-1
例如：可以产生如下seq
>chain_A
 TSLRDLIPKH KFDNSTIDQL CKLIDNEIEP IIFDLLKWLQ DYNWPIAKDI LPVVVLHQSI
 AMPHILTILQ GNDIMWKYWV IKLMIPYLIY PNKQLVKSEL ERLSSLEIIN EDIREIVNLS
 KDSLHFTI
>chain_B
 TSLRDLIPKH KFDNSTIDQL CKLIDNEIEP IIFDLLKWLQ DYNWPIAKDI LPVVVLHQSI
 AMPHILTILQ GNDIMWKYWV IKLMIPYLIY PNKQLVKSEL ERLSSLEIIN EDIREIVNLS
 KDSLHFTI

二：找到正确的seq文件。假设如下：
>cc.data

MTSLRDLIPK HKFDNSTIDQ LCKLIDNEIE PIIFDLLKWL QDYNWPIAKD ILPVVVLHQS
IAMPHILTIL QGNDIMWKYW VIKLMIPYLI YPNKQLVKSE LERLSSLEII NEDIREIVNL
SKDYLHFYYP

三：利用ClustalW2 - Multiple Sequence Alignment进行序列比对
http://www.ebi.ac.uk/Tools/msa/clustalw2/
>chain_A
 TSLRDLIPKH KFDNSTIDQL CKLIDNEIEP IIFDLLKWLQ DYNWPIAKDI LPVVVLHQSI
 AMPHILTILQ GNDIMWKYWV IKLMIPYLIY PNKQLVKSEL ERLSSLEIIN EDIREIVNLS
 KDSLHFTI
>cc.data
MTSLRDLIPKHKFDNSTIDQLCKLIDNEIEPIIFDLLKWLQDYNWPIAKDILPVVVLHQSIAMPHILTILQGNDIMWKYWVIKLMIPYLIYPNKQLVKSELERLSSLEIINEDIREIVNLSKDSLHFTIPDKHN
这将得到如下结果

CLUSTAL 2.1 multiple sequence alignment


chain_A         -TSLRDLIPKHKFDNSTIDQLCKLIDNEIEPIIFDLLKWLQDYNWPIAKDILPVVVLHQS 59
cc.data         MTSLRDLIPKHKFDNSTIDQLCKLIDNEIEPIIFDLLKWLQDYNWPIAKDILPVVVLHQS 60
                 ***********************************************************

chain_A         IAMPHILTILQGNDIMWKYWVIKLMIPYLIYPNKQLVKSELERLSSLEIINEDIREIVNL 119
cc.data         IAMPHILTILQGNDIMWKYWVIKLMIPYLIYPNKQLVKSELERLSSLEIINEDIREIVNL 120
                ************************************************************

chain_A         SKDSLHFTI----- 128
cc.data         SKDSLHFTIPDKHN 134
                *********

四：将该文件下载
利用chainsaw对pdb文件进行修改。脚本如下
chainsaw xyzin 2010-05-HOME-pro_refine_8.pdb alignin seq.aln xyzout test_chainsaw.pdb <<eof
END
eof
就ok了，用修改后的pdb文件的seq再进行aln发现

CLUSTAL 2.1 multiple sequence alignment


cc.data         MTSLRDLIPKHKFDNSTIDQLCKLIDNEIEPIIFDLLKWLQDYNWPIAKDILPVVVLHQS 60
chain_B         -TSLRDLIPKHKFDNSTIDQLCKLIDNEIEPIIFDLLKWLQDYNWPIAKDILPVVVLHQS 59
chain_A         -TSLRDLIPKHKFDNSTIDQLCKLIDNEIEPIIFDLLKWLQDYNWPIAKDILPVVVLHQS 59
                 ***********************************************************

cc.data         IAMPHILTILQGNDIMWKYWVIKLMIPYLIYPNKQLVKSELERLSSLEIINEDIREIVNL 120
chain_B         IAMPHILTILQGNDIMWKYWVIKLMIPYLIYPNKQLVKSELERLSSLEIINEDIREIVNL 119
chain_A         IAMPHILTILQGNDIMWKYWVIKLMIPYLIYPNKQLVKSELERLSSLEIINEDIREIVNL 119
                ************************************************************

cc.data         SKDSLHFTIPDKHN 134
chain_B         SKDSLHFTI----- 128
chain_A         SKDSLHFTI----- 128
                *********     

果然已经改过来了。Yeah！