May 20 2013
How to perform interactive modeling:
What you need before you can undertake interactive modeling:
You can use an alignment you have constructed yourself or allow ICM to generate one (referred to as automatic)
An Interactive Modeler's View of the alignment will then be displayed.
Once you have made your interactive model your graphical user interface should look something like this:
What do all the elements of the Modeler's View mean?
You can browse a number of different loop conformations by clicking on the +/- button next to the loop in the modeler view's window. Keep an eye on the colors of the loop residues in the alignment - they are colored red (poor) -yellow - blue (good) depending on how good the omega angles are. The residues in the loops are represented by Alanines for every residue other than Glycine or Proline.
If you want to remodel the loop.
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