The interface is rather self-explanatory. However, here you can find some tips concerning the use of Marvin applets, interactive inspection of the results with Chime functions, and the meaning of some symbols.
Interface for structure submission
Detailed documentation of the Java molecular editor is available from ChemAxon web site. You can go to this web site by clicking on the 'Help' button. A frequent question is how to define stereochemistry - double click over the bond button on the left panel and choose the type of bond.
Beyond the obvious functions of the editor, it is possible to import a mol file to the editor. You have to click on at the top left to detach the applet, then go to the Edit menu, and choose Source. Clear the window and paste the entire content of your mol file. Then choose Import in the File menu, and click again on to attach the applet.
Interface for visualization of predictions
- Query structure: is displayed as originally drawn using the Marvin applet at the top left. By double-clicking on it, a window is open for edition of the structure. When you are ready, close the window and click on Re-Estimate. You can visualize the list of hydrogen numbers (IDs) on the 2D query structure with the Java applet. Here is how. Before submitting the structure, detach the applet ( ), go to the Edit menu, and choose H Atoms -> Add. This will add all the hydrogens to the structure. In the page with the results, double click on the 2D structure, add all hydrogens as before, then go to the View menu, choose Misc, and select Atom numbers.
- 3D model: is generated by CORINA and is displayed at the top center. It is visualized with Chime plugin and it is a interactive rotatable model - by moving the mouse with the left button down you can rotate the structure. Right button displays the usual Chime menu. Moving the mouse with Shift button pressed, zooms the model. If you click over an hydrogen atom, the predicted chemical shift will be displayed above the model (on Netscape it will also appear in the 3D model near the atom).
- Buttons: several buttons are displayed in the nearby of the 3D structure, and before each hydrogen atom in the list of predicted chemical shifts. Some control the visualization of the predicted chemical shifts in the 3D model. Others control the visualization of the hydrogen atoms numbers (IDs) in the 3D model, in order to assign the atoms to the predictions shown as a list on the right.
- List of predicted chemical shifts: is displayed at the top right in plain text format. Each line contains information for one proton, and includes: a) the number of the H atom, b) a button to highlight the corresponding atom in the 3D structure, c) the predicted chemical shift, d) the classification of the proton as aromatic, pi non-aromatic, aliphatic, or rigid aliphatic, and e) estimation of the reliability of the prediction symbolized by green, yellow or red (high, medium or low reliability).
- Spectrum-like plot: is displayed at the bottom by Chime plugin. It is calculated from the predicted chemical shifts, coupling constants and estimated miltiplicity. It is linked to the 3D model at the top in such a way that when you click on a signal, the corresponding protons are highlighted in the structure at the top.
To print the spectrum you may need to transfer the screen image (PrtScn) to an image visualizer.