Mercury 101

So you’re working on your Molecule of the Week assignment and you’re looking at your molecule in Mercury and thinking Wow this is hideous. How am I going to make this look presentable? If you’re not familiar with Mercury, the program seems a bit complicated with letters and buttons all over the place. Hopefully some of these tips will help clear things up, and you’ll get a pretty picture in the end.

Let’s Start with a before picture:

This was my Molecule of the Week before any editing

This picture is chaotic and extremely confusing. So now what…

  1. You can hide all of the hydrogens on your molecule in one simple click. In the bottom right hand corner (directly below the picture) under options uncheck “Show Hydrogens.”
  2. You can change how the atoms/bonds look. In the upper left hand corner next to “Style” there’s a drop down menu giving you 4 different options. If you have nothing highlighted the entire molecule’s style will change when you select any of these. However, you can change atoms individually or as groups. Just click the center of the atom(s) and then choose which style you like. There’s no need to hold down any keys when selecting multiple atoms, and you may have to rotate the molecule slightly to be able to select the atoms. Don’t worry, your previously selected atoms will not be deselected by this action, rotate away.
  3. You can hide atoms. Select the atoms you don’t want to see. Go to Display > Show/Hide > Atoms > Select Hide > Okay. The atoms magically disappear, it’s fantastic, and gets rid of “floaters” in your image instantly clearing things up. If you made a mistake, you can go to Edit > Undo, or you can go to Display > Show All and start over.
  4. You can rotate the image without having to click and move the cursor. Up at the top right above the actual image there is a set of buttons “a b c a* b* c*” These are comparable to the x,y,z axes and when you click them your molecule is aligned accordingly. To the right of these commands are x- x+ y- etc… These nudge your molecule slightly in either the positive/negative x y or z direction. The last commands rotate the molecule 90 degrees with respect to the axes. You can also translate your molecule to the left, right, up, or down by clicking on the arrows.
  5. You’ll probably want to zoom in to make your molecule as clear as possible. Just click the zoom buttons on the upper right.

After these 5 steps you’ll end up with a beautiful molecule:

These are just a few simple little tricks that should help you create a professional looking picture. Clearly there are many other things Mercury has to offer, however I am not familiar with the program entirely. Therefore, I would like to ask all of you to comment here when you discover new tricks. Good luck, and don’t be afraid to click things. I discovered a lot of tricks simply by trial and error.

Comment (1) Add yours ↓
  1. nharmuth

    now that the pressure is on to get some posts up make sure you guys refer to this post when working on your MotW.. i think it’ll save you a lot of time and perhaps some frustration. And if you discover anything else useful in the process comment here!

    29 October 2008

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