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.

譯文如下：

3.4. 圖形和圖像

3.4.1. 繪制一個繞柱螺旋鏈

在Olex2中可以繪制分子繞柱螺旋排列圖，但這有點棘手。

選擇原子的視圖樣式。這最好在不對稱單元中進行設(shè)置。

使用pack指令將該結(jié)構(gòu)進行足夠大的堆積，例如pack 20。這將產(chǎn)生一個相當(dāng)混亂的圖像，因為原來的不對稱單元是隨機排列的：

接下來，找到一個顯示螺旋軸“正面”的視圖。可以嘗試matr 1、matr 2和matr 3等指令調(diào)整視圖，最終得到如下更整潔的視圖：

使用SHIFT+Left Mouse組合在中間部分繪制一個矩形方框。這將選擇矩形框下的所有原子，直到晶胞(即，也將選擇當(dāng)前不可見的原子)。

現(xiàn)在通過鍵入sel -i(或者快捷鍵Ctrl+I)進行反選，按下Delete鍵刪除不想要的原子。最后將得到如下結(jié)果：

接下來，選擇用于定義希望繪制的軸的所有原子。在本例中，鍵入sel $M $N并回車。這將選擇視圖中所有的金屬(Metal)原子和所有的氮(Nitrogen)原子。選中這些原子后，鍵入line并回車。當(dāng)你對分子進行轉(zhuǎn)動(或使用matr 1指令調(diào)整視角)，你可以看到位于中心的那根線。在該線上單擊鼠標(biāo)左鍵將其選中，鍵入brad 10并回車使其更粗。在該線上單擊鼠標(biāo)右鍵，然后選擇Graphics > Draw style，在彈出的對話框中進行設(shè)置，使其達(dá)到你所希望的結(jié)果。

如果你希望金屬陽離子更大，鍵入sel $M并回車選中所有金屬陽離子后鍵入brad 1.8并回車。此處同時更改了中心柱的顏色。

上圖通過matr 1后跟rota 3 90對視角進行了調(diào)整。

輔助視頻如下：

Olex2作圖(繞軸螺旋鏈)

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

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