Graphics and Images

Draw a Helical Chain around a Rod

Drawing a helical arrangement of molecules around a rod can be done in Olex2, but it’s a bit tricky to do.

Choose the view style of your atoms. This is best done when looking at the asymmetric unit.

Pack a sufficiently large junk of this structure, say pack 20. This gives you a rather messy picture, because the original asymmetric unit was randomly aligned:

Next, find a view that shows the helical axis ‘head-on’. Try matr 1, matr 2, and matr 3, which gives this muchmore tidy view:

Using SHIFT+Left Mouse, draw a rectangle over the middle portion here. This will select all atoms under the rectangle, all the way down the cell (i.e. will also select the atoms that are not currently visible.

Now invert the selection, by typing sel –i, and delete any unwanted atoms. You should end up with this:

Now select all atoms defining that axis you want to draw. In this case, type sel $M $N. This will select all Metal atoms and all Nitrogen atoms. With these atoms selected, type line. When you turn the molecule areond (or align it with matr 1 ), you can see the line in the center. Left-click on the line, and type brad 10, to make it thicker. Right-click on the line, then select Graphics > Draw Style and play with the options there to make it look like you want it to look.

If you wanted the metal ions to be bigger, type sel $M flollowd by brad 1.8. I have also changed the colour of the rod here.

The above alignment was achieved with matr 1 followed by rota 3 90.

译文如下：

3.4. 图形和图像

3.4.1. 绘制一个绕柱螺旋链

在Olex2中可以绘制分子绕柱螺旋排列图，但这有点棘手。

选择原子的视图样式。这最好在不对称单元中进行设置。

使用pack指令将该结构进行足够大的堆积，例如pack 20。这将产生一个相当混乱的图像，因为原来的不对称单元是随机排列的：

接下来，找到一个显示螺旋轴“正面”的视图。可以尝试matr 1、matr 2和matr 3等指令调整视图，最终得到如下更整洁的视图：

使用SHIFT+Left Mouse组合在中间部分绘制一个矩形方框。这将选择矩形框下的所有原子，直到晶胞(即，也将选择当前不可见的原子)。

现在通过键入sel -i(或者快捷键Ctrl+I)进行反选，按下Delete键删除不想要的原子。最后将得到如下结果：

接下来，选择用于定义希望绘制的轴的所有原子。在本例中，键入sel $M $N并回车。这将选择视图中所有的金属(Metal)原子和所有的氮(Nitrogen)原子。选中这些原子后，键入line并回车。当你对分子进行转动(或使用matr 1指令调整视角)，你可以看到位于中心的那根线。在该线上单击鼠标左键将其选中，键入brad 10并回车使其更粗。在该线上单击鼠标右键，然后选择Graphics > Draw style，在弹出的对话框中进行设置，使其达到你所希望的结果。

如果你希望金属阳离子更大，键入sel $M并回车选中所有金属阳离子后键入brad 1.8并回车。此处同时更改了中心柱的颜色。

上图通过matr 1后跟rota 3 90对视角进行了调整。

辅助视频如下：

Olex2作图(绕轴螺旋链)

https://www.bilibili.com/video/BV1TA411874A

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