How to use the molecule editor

Worked example:

changing the input file for a 360° rotation around C-C bond in ethane into one for propane

This worked example describes step-by-step what to do to change the file "360° rotation around C-C bond in ethane" to a 360° rotation around one of the C-C bonds in propane using the molecule editor.

1. On the Submit a molecule page, click on edit & submit file behind "360° rotation around C-C bond in ethane".
   The top part of the page that you will get, looks like this:
   
   
   Click on the image to see a larger screen-capture
   
   On that page, you can rotate the Chime-structure in the usual way, by moving the mouse while keeping the left mouse button down.
   
   
2. You can select the atom you want to change by single-clicking on it with the left mouse button. Since we want to build propane, just select one of the hydrogen atoms.
   (Note: in the SG and Mac versions of Chime, the +y and -y coordinates may be interchanged; imagine a horizontal mirror plane right through the structure, or place, by rotating the molecule, the atom to be substituted more or less on this x axis.)
   The top of the screen will then look like this (the atom number can be different, but it should be an H):
   
   
   Click on the image to see a larger screen-capture
   
   
3. The pull-down menu already displays CH3, and that's indeed what we want to change the hydrogen atom into. If you would like to change it into something else (Cl, Br, OH, NH₂, CH=O, ...), you can change it there. In this example, we want to have propane, so CH3 suits us fine. Now, click on the change it! button. The changes will be made, and the top of the page will then look like this:
   
   
   Click on the image to see a larger screen-capture which also shows the changes in the datafile
   
   ... and there it is, propane...!
   (Note: not if you use Internet Explorer4.0, which, for unknown reasons refuses to update the structure. The files are OK though, so you can continue, or edit the text window.)
   However, if you regret making propane, and wanted to make chloroethane for example, or if you made some other mistake, you can undo the last change by clicking the undo button. Note that you can only undo one step!
   
   Another option is to colour the changed atom blue. This comes in handy if you want to make another change. For example, suppose you want to change the propane into n-butane. To make sure that the rotation to be calculated will be around C2-C3, you have to attach another methyl group to the other end of the molecule, and not to the group you just attached.
   
   
4. To submit this calculation, go to the bottom of the page and click on create the batchfile:
   
   
   Click on the image to see a larger screen-capture
   
   
5. The next page shows your dataset a last time before the calculation is started. You can choose whether your calculation will run in the short queue or in the medium queue. Most of the time, the short queue will be the right choice. Only if the calculation takes more than 10 minutes, the medium queue will be needed. Click on submit your job to start the calculation.
   
   
   Click on the image to see a larger screen-capture
   
   
6. While the calculation is running, you will get a screen with the contents of the directory in which the calculation is performed. This screen updates every ten seconds and looks like this:
   
   
   Click on the image to see a larger screen-capture
   
   If you get a mopac.out file immediately, and no mopac.temp file, an error was detected in the input file. Read the mopac.out file for details.

7. When the calculation is finished and no errors have occurred, you will get the results of your calculation in a web-page like this:
   
   
   Click on the image to see a larger screen-capture
   
   The structure can be examined step-by-step; the numbers on the x-axis of the energy profile correspond to the "frame" of the animation. Below are links to the input-file (mopac.dat), the out-file (mopac.out) and the arc-file (mopac.arc), as well as a link go back to the molecule editor using the current input file as a starting file.

Okay, I think I understand it, let me try it!