解析蛋白晶体结构，为了获得稳定的蛋白结构。往往需要突变，以稳定蛋白结构。

可以通过consensus view,来观察序列的差异。

为了进一步定量计算其差异性，我们计算3组RMSD

•1.整体叠合，整体RMSD

•2.整体叠合，口袋RMSD

•3.口袋叠合，口袋RMSD

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尽管schrodinger 中有多种叠合,ALIGN的方法，比如align binding sites; protein structure alginment;superposition;conformer cluster;。 但是能完全胜任上述任务的只有SUPERPOSITION。

1 align binding sites

This script performs a pairwise superposition of multiple structures using the C-alpha atoms of selected residues. The reference structure for the alignment is the first structure in the input file. The C-alpha atoms used for the alignment come from residues within the specified cutoff distance from the ligand in the reference structure. Alternatively, a list of residues may be given for the alignment, which must correspond to residues in the reference structure. C-alpha atoms in the structures that are aligned that are greater than the specified distance from any C-alpha in the reference are not considered in the alignment. The RMSD matrix for the alignment is written to the file jobname-matrix.csv in three columns: the indexes for the structures, then the RMSD value. The syntax is:

align_binding_sites [options] input-files

If you specify more than one input file, the reference structure is the first structure in the first file. For a description of the options, run the command with the -h option.

-rmsdatoms RMSDATOMS  Group of atoms over which to compute the RMSD matrix.
                       The default is Calpha carbons, and choices are calpha,
                       backbone, sidechain, heavy and all. This option does
                       NOT affect the actual atoms used for alignment nor the
                       RMSD values that are reported as "Post-SKA RMSD" or
                       "Final RMSD" in the .log file - only the RMSD matrix
                       values reported in the .log and -matrix.csv file are
                       affected by this flag. The "Post-SKA RMSD" and "Final
                       RMSD" values reported in the .log file during the
                       alignment step are for the Calpha atoms actually used
                       in the alignment. Note that sidechain, heavy, and all
                       should only be used if all proteins will have
                       identical residue types in the binding site.

基于口袋叠合后对口袋RMSD的计算。 无法实现功能2。在图形界面无法更改rmsdatoms参数。

2. conformer cluster 需要是同一个蛋白的不同构象，如果有突变，无法计算RMSD

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整体叠合，整体RMSD,选择all ,然后允许位置align。

在这个基础上，选择口袋氨基酸，不允许变化，选择口袋氨基酸就可以计算整体叠合，口袋RMSD 。

口袋叠合，口袋RMSD，选择口袋氨基酸，允许口袋变换就可以计算了。