原文如下：

Work with idealised and regularised groups and AFIX instructions

There are several commands in Olex2/shelx which allow creating and managing the idealised or regularised groups in Olex2. These groups are typically used when there is a disorder in place or when the group is not behaving due to insufficient or weak data.

There are two ways to use regular group in the refinement: one would be to use restraints and the other - to use pre-computed or average geometries (idealised) which occur in other structures. In the case when there is not enough data available, the use of latter approach is beneficial since it reduces the number of parameters to be refined. There are 6 parameters normally refined for an idealised group - the position (x, y, z) and three angles (AFIX 6). In some cases the number of parameters can be increased to 7 - when the size of the groups is refined as well (AFIX 9). In other cases further constraints can be used and the number of refinable parameters reduced to 4, like in the case of -C-CF3 group, where the position of the CF3 group is refined, but only one angle - the rotation around the C-C bond is refined (AFIX 7); in this case the number of parameters can be extended to 5, when the C-F bond lengths are also refined (AFIX 8). In some case only 3 positional parameter can be refined (AFIX 3) which can be used with -X-CH3 groups in staggered positions and when refining the C-H bond lengths (AFIX 4) the number of parameters increases to 4.

It worth noting that shelx AFIX number consists of two parts - the first one (m, unless 0) is responsible for the re-idealisation of the group and the other one (n) is responsible for how the group is refined. The re-idealisation of the groups happens before every refinement cycle and is required due to the precision being lost during the file output and input operations. Thus the idealised groups which are refined without the re-idealisation tend to get slightly distorted after a series of refinement procedures.

The idealised groups are extensively exploited when refining hydrogen atoms and typically there are no issues (unless when the atom connectivity changes during the refinement) occur. The use of more complex groups, like Ph or Cp requires more attention. One of the potential pitfalls are the intersecting idealised groups - when this happens, the refinement cannot proceed. To avoid this situation, each idealised groups should have its own set of atoms which can be generated in Olex2 using various splitting modes and/or 'split' function.

Here is a list of commands and modes useful for this particular section:

Afix, HAdd, ImportFrag, ExportFrag, Split, mode fit -s, mode split, split, Fvar, Part. Most of these command are available from the GUI. These commands are suitable for placing restraints to regularise the groups: Sadi, RRings, ImportFrag.

译文如下：

3.19. 用AFIX命令处理理想化和规则化的基团

Olex2/shelx中有数个指令允许在Olex2中创建和处理理想化或规则化的基团。这些基团的处理通常在无序或由于数据不足或较弱而导致基团不正常时使用。

在精修中有另种方法使用规则基团：一种是使用限制，另一种是使用在其他结构中出现的预先计算或一般几何(理想化)。在没有足够数据可用的情况下，使用后一种方法是有益的，因为它减少了要精修的参数的数量。对于一个理想化的基团，通常有6个参数：位置(x, y, z)和三个角度(AFIX 6)。在某些情况下，参数的数量可能增加到7：当基团的大小也被精修时(AFIX 9)。在其他情况下，可以使用进一步的约束，并且可精修参数的数量可以减少到4，例如在-C-CF3基团的情况下，CF3基团的位置被精修，但只有一个角——绕C-C键的旋转被精修(AFIX 7)；在这种情况下，参数的数量可以扩展到5，当C-F键键长也被精修时(AFIX 8)。在某些情况下，只有3个位置参数可以精修(AFIX 3)，它可以用于处理位于交错位置的-X-CH3基团，并且当精修C-H键键长(AFIX 4)时，参数的数量增加到4。

值得注意的是，shelx AFIX参数由两部分组成：第一部分(m, 除非为0)负责对基团的重新理想化，另一部分(n)负责如何精修该基团。基团的重新理想化发生在每次精修循环之前，并且由于在文件输出和输入操作期间丢失了精度，因此需要重新理想化。因此，未经重新理想化的理想化基团在经过一系列精修过程后，往往回发生轻微的扭曲。

理想化基团在精修氢原子时被广泛利用，通常不会出现问题(除非精修过程中原子连接性发生变化)。使用更复杂的基团，例如Ph和Cp，需要更多的注意。其中一个潜在的困难是交叉的理想化基团——当这种情况发生时，精修就无法进行。为避免这种情况，每个理想化基团应该有自己的原子集，这些原子集在Olex2中可以使用各种拆分模式和/或'split'功能生成。

以下是对该特定部分有用的指令或模式列表：

Afix, HAdd, ImportFrag, ExportFrag, Split, mode fit -s, mode split, split, Fvar, Part.其中大多数指令都可以在GUI中使用。这些指令适用于放置限制以调整基团：Sadi, RRings, ImportFrag.

相关辅助视频：

2.6-处理无序模型-约束和限制(AFIX)

https://www.bilibili.com/video/BV1Eh411k7Lh

Olex2中AFIX 66(AFIX 56及AFIX 116)用法简演

https://www.bilibili.com/video/BV1Ak4y1k7dK

Olex2中使用AFIX 66指令补全苯环原子

https://www.bilibili.com/video/BV1AQ4y1T7ej

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