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

譯文如下：

3.10. 堆積或生長分子

處理結構時，堆積和增長是基本操作。

Olex2中有數(shù)種指令用于增長和堆積分子。第一個指令為'grow'，該指令將不對稱單元中的所有原子進行增長。Grow指令將產(chǎn)生分子，直到所有新的可用的生長矩陣僅在平移部分不同，這將為離散分子創(chuàng)建完整的原子集，并未聚合物結構生成相當大的片段。若需要使用特定對稱操作，則'sgen'指令將非常有用，例如：

>>sgen 1556 $N

或

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

將使用x,y,z+1對稱操作碼(相同對稱操作碼，x,y,z始終是Olex2中的第一個操作碼)生成所有氮原子。若未提供原子，則所有原子都將產(chǎn)生。也可單擊可以增長的原子，然后從菜單中選擇'Grow'選項。

若要查看加載結構的操作碼集合，請使用：

>>lstsymm

還有一種增長模式(在相關表格中查看此模式的所有相關選項)，它提供了有關可以生長的鍵的可視化和度量信息。該模式允許一次使用一個對稱操作碼：

>>mode grow

增長指令僅產(chǎn)生可增長的片段；有時需要同時產(chǎn)生不對稱單元的其余片段，例如在主片段增長后，所有相關的溶劑分子也需要產(chǎn)生。為此，可以使用'grow -w'指令，它將增長不對稱單元中的其余片段。

使用'envi'指令還可以找到有關可以增長原子(若處于特殊位置)或鍵的矩陣信息。要找出處于特殊位置的原子，請使用'degen'指令，該指令將打印原子位置的多重性(除非它是1)。

pack指令可用于堆積分子或指定原子。例如：

>>pack R

產(chǎn)生質量中心在R半徑范圍內(nèi)的分子

>>pack cell

顯示單胞內(nèi)容。用'grow -w'來顯示所有對單胞有貢獻原子的分子。

>>pack $Fe

僅堆積指定原子，可添加'-c'選項用于指定當前模型不被清除。

>>mode mobe [-c]

一旦一個片段的原子被選中，此模式將復制(若提供'-c'選項)或移除任意其他片段(單擊)盡可能靠近所選原子。

>>mode pack

顯示不對稱單元為四面體的集合，單擊該四面體可使用特定轉換生成不對稱單元。

諸如'pipi'和'htab'的結構分析指令，若同時提供'-g'選項同樣可用于增長分子并使得某些特定相互作用可視化。

最后，要顯示不對稱單元，請鍵入：

>>fuse

本文輔助視頻如下：

Olex2中錯位面對面π-π堆積中的滑移角的計算

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

Olex2中定向堆積以及特定軸的畫法

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

Olex2+PS繪制單胞堆積圖

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

公眾號文章鏈接：

https://mp.weixin.qq.com/s?__biz=MzU0NjkzMTM1MQ==&mid=2247485350&idx=5&sn=2c02eb5938f163bd2215ec9a701e58f1&chksm=fb57505ecc20d948c1da28fbb6d4e46fd67b1d6d0f6daa74235a8644fdd6b382eaa13d40dcc6&token=1126004319&lang=zh_CN#rd