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

譯文如下：

3.7. 故障排除

3.7.1. 疊加分子

Olex2提供了數(shù)種工具用于匹配/對(duì)齊/重疊片段或分子。若片段具有相同的連接性，則用戶可通過(guò)鍵入“match”指令用于自動(dòng)匹配分子。Olex2將搜索具有相同連接性*的分子圖形并將它們對(duì)齊，以?為單位打印相應(yīng)的RMSD。若結(jié)構(gòu)中有兩個(gè)以上的片段，則可以分別選擇一對(duì)片段中的一個(gè)原子，并鍵入以下指令以僅匹配所選片段：

>>match

match宏還可使用“-i”選項(xiàng)。當(dāng)給定此選項(xiàng)時(shí)，程序?qū)L試以反轉(zhuǎn)坐標(biāo)匹配第一個(gè)片段和第二個(gè)片段。結(jié)果將打印為RMSD和轉(zhuǎn)換矩陣，使用“-a”選項(xiàng)對(duì)齊片段。

請(qǐng)注意，若分子存在無(wú)序或具有更高對(duì)稱性，自動(dòng)匹配可能會(huì)失敗。此外，若結(jié)構(gòu)中存在Q峰，則應(yīng)將其隱藏(Ctrl+Q)或使用以下指令將其刪除：

>>kill $Q

由于圖形匹配算法的執(zhí)行不使用任何模式識(shí)別進(jìn)行優(yōu)化，因此高對(duì)稱性可能會(huì)引入大量可能的圖形組合(例如每個(gè)甲基以6(3!)的倍數(shù)增加組合數(shù)量)，建議隱藏氫原子(Crtl+H)。如果這沒有幫助，可能需要手動(dòng)更改原子類型以打破對(duì)稱性。

若由于片段連接性的差異導(dǎo)致自動(dòng)對(duì)齊失敗，用戶可能需要選擇其中一個(gè)片段的至少三個(gè)原子以及另一個(gè)片段中按匹配順序選擇相同數(shù)量的原子并鍵入：

>>match

以使片段僅以所選原子進(jìn)行匹配。

程序同時(shí)提供了一個(gè)匹配模式，其激活可通過(guò)鍵入：

>>mode match

該模式允許最多三對(duì)原子進(jìn)行交互式匹配。第一對(duì)原子被疊加，第二對(duì)原子通過(guò)旋轉(zhuǎn)以使第二對(duì)原子之間的距離最小化，第三對(duì)原子通過(guò)繞第一對(duì)原子和第二對(duì)原子之間形成的線旋轉(zhuǎn)以使第三對(duì)原子之間的距離最小化。

Olex2同樣提供了一種方式用于加載額外的結(jié)構(gòu)到屏幕中。該結(jié)構(gòu)同樣可用于所有上述描述的匹配程序。若要加載額外的結(jié)構(gòu)，請(qǐng)鍵入：

>>@reap -* [file_name]

若未給定文件名，將打開“Open File”對(duì)話框。

*片段連接性可通過(guò)使用Addbond、Dlebond和Conn指令進(jìn)行調(diào)整。例如，如果所考慮的化合物是具有兩個(gè)或更多相同配體的金屬配合物，則可以通過(guò)選擇金屬原子并鍵入以下指令將配體與金屬“分離”：

>>conn 0

本文輔助視頻如下：

Olex2視頻教程——Olex2作圖之結(jié)構(gòu)重疊對(duì)比

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

公眾號(hào)文章鏈接：

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