Secretary's Bio/Chem-Info Journal #16 Observing Ligand Binding Sites with UCSF Chimera

By using UCSF Chimera, you can visualize 3D structures.

Preparation

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This time, we will use the structure of the β2 receptor "3SN6". Download the PDB file in advance.

This is what it looks like when opened in UCSF Chimera.

It is convenient to use a 3-button mouse for operations. The operation methods are summarized below; you should get used to these first.

Rotate molecule: Left-click + drag

Translate molecule: Wheel button + drag

Zoom in/out molecule: Right-click + drag or scroll wheel

Select atom: Ctrl key + left-click

Add to selection: Ctrl key + Shift key + left-click

Expand/shrink selection: (Expand) Up arrow key, (Shrink) Down arrow key

Deselect: Ctrl + left-click on an empty space or use the menu "Select" → "Clear Selection"

Here is the view after changing the orientation.

Presets contains various templates, and among them, using Interactive1 allows for color-coding.

Displaying the ligand structure

Select→Residue→(Ligand Name) to select the ligand. At this time, clicking Action→Focus will center the ligand as shown below.

This time, I will clearly display the surrounding residues (within 4Å) for docking.

To specify surrounding residues, select the ligand with Select→Residue→(Ligand Name), then use Select→Zone to bring up the following screen. Change the settings as shown in the red box and click OK to select the surrounding residues.

Once selected, use Action→Atoms/Bonds→ball & stick to make the surrounding residues easier to see.

For the ligand display, return it to sticks with Action→Atoms/Bonds→stick, and color-code it with Action→Color→by element.

Next, display the residue information. Select surrounding residues with Select→Zone, and display them using Action→Label→residue→name+specifier.

Here, you can change the font of the text from Action→Label→option.

Next, display the hydrogen bonds.

Select the ligand, and the following screen will appear via Tools→Structure Analysis→FindHBond. Change the settings in the red box and click.

Action→Libbon→hide shows the result with the ribbon structure hidden. This makes the structure around the ligand easier to see.

When finished, save the file using File→Save Session As ....

The table of contents for this article is here: