The Molecules section of the NovaDock Report displays information about the receptor and ligand structures that were used as inputs in the NovaDock prediction. To view or hide this section of the report, click on the expand arrow (small blue triangle) in its header.
In the Molecules section, thumbnail preview images show the input molecules rendered in the “ribbon” motif, with the receptor shown in green, and the ligand shown in yellow.
Because the original structures were user-supplied, they may have had missing atoms or residues, or non-standard residues. The structures shown in the Molecules section are the “repaired” versions of those files (if any repairs were made). If any repairs were made, they will be listed in the Repairs section of the Details panel.
Thumbnail previews are interactive and can be controlled with the mouse or with the links provided:
| Task | How to… |
|---|---|
| To rotate the model manually | Slide the mouse laterally while holding down the left mouse button. |
| To spin the model around its axis automatically | Click the link Spin the model to spin the model slowly clockwise, as viewed from above. Once the model is spinning, this link changes to Stop spinning the model. |
| To open the model as a new Protean 3D document | Click the link Open model in new document. |
| To zoom in/out | Use the mouse’s scroll wheel. |
Information about each molecule appears to the right of its thumbnail preview.
| Item | Description |
|---|---|
| Receptor/Ligand | The name of the input file specified as the receptor or ligand when setting up a NovaDock prediction. |
| Proposed contacts | Number of residue contacts, if any, proposed by the user when initiating the NovaDock prediction. |
| Chain | The letter representing the chain name. Clicking the chain name link selects the receptor and/or ligand in the two thumbnail images. The selected chain(s) will be highlighted in light blue. |
The next section of the NovaDock Report is the Model Overview section.
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