原文如下：

Troubleshooting

Overlay molecules

Olex2 provides several tools to match/align/overlay fragments or molecules. If the fragments have the same connectivity, the user can just type 'match' for automatic matching of the molecules. Olex2 will search for molecular graphs of the same connectivity* and align them, printing corresponding RMSD in angstroms. If the structure has more than two fragments, one atom of pair of fragments can be selected and the following command issued to match the selected fragments only: 

>>match

The match macro also takes the '-i' option. When this option is given, the procedure will try to match the first fragment and the second one with the inverted coordinates. The result will be printed as the RMSD and the transformation matrix, use the '-a' option to align the fragments. 

Note that if your molecule is disordered or has high symmetry, the automatic matching might fail. Also if there are Q-peaks in the structure, they should be hidden (Ctrl+Q) or deleted using the following commands: 

>>kill $Q 

Since graph matching algorithm implementation does not use any pattern recognition for the optimisation, high symmetry may introduce huge number of possible graph permutations (like each CH3 group increases the number of permutations by a factor of 6 (3!)), it is recommended to hide the H atoms (Ctrl+H). If this does not help, a manual change of atom types may be required to break the symmetry. 

If automatic alignment fails due to the difference in the connectivity of the fragments, the user might select at least three atoms of one fragment and the same number of atoms in another fragment in matching sequence and type 

>>match 

to match fragments using only the selected atoms. 

There is also a matching mode, which can be activated by typing:

>>mode match 

This mode enables interactive matching by a maximum of three pairs of atoms. The first pair of atoms are superimposed, the second one causes the rotation to minimize the distance between the atoms of the second pair, the third pair causes rotation around the line formed by the first and second pair to minimize the difference between the atoms of the third pair. 

Olex2 also provides a way to load an extra structure on screen. That structure can also be used in all the matching procedures described above. To load an extra structure, type: 

>>@reap -* [file_name] 

if the file name is not given, the 'File Open' dialog will apear. 

*The fragment connectivity can be adjusted using the AddBond, DelBond and the Conn commands. For example if the compound under the consideration is a metal complex with two or more identical ligands, the ligands can be 'detached' from the metal by selecting the metal atom and typing 

>>conn 0

译文如下：

3.7. 故障排除

3.7.1. 叠加分子

Olex2提供了数种工具用于匹配/对齐/重叠片段或分子。若片段具有相同的连接性，则用户可通过键入“match”指令用于自动匹配分子。Olex2将搜索具有相同连接性*的分子图形并将它们对齐，以Å为单位打印相应的RMSD。若结构中有两个以上的片段，则可以分别选择一对片段中的一个原子，并键入以下指令以仅匹配所选片段：

>>match

match宏还可使用“-i”选项。当给定此选项时，程序将尝试以反转坐标匹配第一个片段和第二个片段。结果将打印为RMSD和转换矩阵，使用“-a”选项对齐片段。

请注意，若分子存在无序或具有更高对称性，自动匹配可能会失败。此外，若结构中存在Q峰，则应将其隐藏(Ctrl+Q)或使用以下指令将其删除：

>>kill $Q

由于图形匹配算法的执行不使用任何模式识别进行优化，因此高对称性可能会引入大量可能的图形组合(例如每个甲基以6(3!)的倍数增加组合数量)，建议隐藏氢原子(Crtl+H)。如果这没有帮助，可能需要手动更改原子类型以打破对称性。

若由于片段连接性的差异导致自动对齐失败，用户可能需要选择其中一个片段的至少三个原子以及另一个片段中按匹配顺序选择相同数量的原子并键入：

>>match

以使片段仅以所选原子进行匹配。

程序同时提供了一个匹配模式，其激活可通过键入：

>>mode match

该模式允许最多三对原子进行交互式匹配。第一对原子被叠加，第二对原子通过旋转以使第二对原子之间的距离最小化，第三对原子通过绕第一对原子和第二对原子之间形成的线旋转以使第三对原子之间的距离最小化。

Olex2同样提供了一种方式用于加载额外的结构到屏幕中。该结构同样可用于所有上述描述的匹配程序。若要加载额外的结构，请键入：

>>@reap -* [file_name]

若未给定文件名，将打开“Open File”对话框。

*片段连接性可通过使用Addbond、Dlebond和Conn指令进行调整。例如，如果所考虑的化合物是具有两个或更多相同配体的金属配合物，则可以通过选择金属原子并键入以下指令将配体与金属“分离”：

>>conn 0

本文辅助视频如下：

Olex2视频教程——Olex2作图之结构重叠对比

https://www.bilibili.com/video/BV1Yb411E7kc

公众号文章链接：

https://mp.weixin.qq.com/s?__biz=MzU0NjkzMTM1MQ==&mid=2247485350&idx=2&sn=a1c11a8904f0f8ed001d4fae96cb7fed&chksm=fb57505ecc20d948169d99898aa3d03abcc60cc80dfe6fdd1785cbc2bb67eca9752520e128f0&token=1126004319&lang=zh_CN#rd