原文如下：

Pack or grow molecule(s)

Packing and growing are fundamental operations when working with structures.

There are several commands in Olex2 to grow and pack molecules. First command is 'grow', this command grows all atoms in the asymmetric unit. Grow command will generate the molecule until all newly available growing matrices differ only by translation part, this will create complete set of atoms for discrete molecules and generate quite a large fragment for polymeric structures. If a particular symmetry operator needs to be used, the 'sgen' command might be useful, for example:

>>sgen 1556 $N

or

>>sgen x,y,z+1 $N

will generate all nitrogen atoms using the x,y,z+1 symmetry operator (the identity operator, x,y,z is always the first operator in Olex2). If no atoms provided, all atoms will be generated. It is also possible to click on an atom which can be grown, and choose the 'Grow' option from the menu.

To find out the set of operators for loaded structure, use:

>>lstsymm

There is also growing mode (look in the table for all related options of this mode), which provides visual and metric information about bonds which can be generated. The mode allows using one symmetry operator a time:

>>mode grow

The growing command generates only fragments which can grow; sometimes it is needed to generate the rest of the asymmetric unit as well, like after growing the main fragment all related solvent molecules need to be generated. For this use the 'grow -w' command, it will grow the rest of the asymmetric unit.

The information about matrices which can grow an atom (if on a special position) or a bond can also be found using the 'envi' command. To find out atoms in special position, use the 'degen' command, which prints the atomic position multiplicity (unless it is 1).

The pack command can be used to pack molecules or particular atoms. For example:

>>pack R

generates molecules which centre of mass is within sphere of R radius

>> pack cell

Shows the content of the unit cell. Use 'grow -w' to show all molecules contributing atoms to the unit cell.

>>pack $Fe

packs only specified atoms, '-c' option can be added to specify that current model should not be cleared.

>>mode move [-c]

once a fragment atom is selected this mode will copy (if '-c' is provided) or move any other fragment (which is clicked) as close to the selected atom as possible.

>>mode pack

Displays asymmetric units as a set of tetrahedron, clicking on which generates the asymmetric unit using that particular transformation.

The structure analysis commands like 'pipi' and 'htab' provided with '-g' option can also be used to grow molecules and visualise some particular interactions.

Finally, to show the asymmetric unit, type

>>fuse

译文如下：

3.10. 堆积或生长分子

处理结构时，堆积和增长是基本操作。

Olex2中有数种指令用于增长和堆积分子。第一个指令为'grow'，该指令将不对称单元中的所有原子进行增长。Grow指令将产生分子，直到所有新的可用的生长矩阵仅在平移部分不同，这将为离散分子创建完整的原子集，并未聚合物结构生成相当大的片段。若需要使用特定对称操作，则'sgen'指令将非常有用，例如：

>>sgen 1556 $N

或

>>sgen x,y,z+1 $N

将使用x,y,z+1对称操作码(相同对称操作码，x,y,z始终是Olex2中的第一个操作码)生成所有氮原子。若未提供原子，则所有原子都将产生。也可单击可以增长的原子，然后从菜单中选择'Grow'选项。

若要查看加载结构的操作码集合，请使用：

>>lstsymm

还有一种增长模式(在相关表格中查看此模式的所有相关选项)，它提供了有关可以生长的键的可视化和度量信息。该模式允许一次使用一个对称操作码：

>>mode grow

增长指令仅产生可增长的片段；有时需要同时产生不对称单元的其余片段，例如在主片段增长后，所有相关的溶剂分子也需要产生。为此，可以使用'grow -w'指令，它将增长不对称单元中的其余片段。

使用'envi'指令还可以找到有关可以增长原子(若处于特殊位置)或键的矩阵信息。要找出处于特殊位置的原子，请使用'degen'指令，该指令将打印原子位置的多重性(除非它是1)。

pack指令可用于堆积分子或指定原子。例如：

>>pack R

产生质量中心在R半径范围内的分子

>>pack cell

显示单胞内容。用'grow -w'来显示所有对单胞有贡献原子的分子。

>>pack $Fe

仅堆积指定原子，可添加'-c'选项用于指定当前模型不被清除。

>>mode mobe [-c]

一旦一个片段的原子被选中，此模式将复制(若提供'-c'选项)或移除任意其他片段(单击)尽可能靠近所选原子。

>>mode pack

显示不对称单元为四面体的集合，单击该四面体可使用特定转换生成不对称单元。

诸如'pipi'和'htab'的结构分析指令，若同时提供'-g'选项同样可用于增长分子并使得某些特定相互作用可视化。

最后，要显示不对称单元，请键入：

>>fuse

本文辅助视频如下：

Olex2中错位面对面π-π堆积中的滑移角的计算

https://www.bilibili.com/video/BV1tz411z79H

Olex2中定向堆积以及特定轴的画法

https://www.bilibili.com/video/BV1TQ4y1N7p2

Olex2+PS绘制单胞堆积图

https://www.bilibili.com/video/BV1F4411b7Q9

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