Here we have a hemoglobin structure with the PDB ID 2hbs. This structure is a mutant which is known
to cause sickle cell disease. Upon examining the interface between the two globular regions,
it appears that certain residues have their side chains shown. To select one of the atoms in these
side chains, use Control plus left click. To broaden the scope of the selection, use
the Up Arrow, and to narrow the scope, use the Down Arrow. You can use the Right
Arrow to invert the selection and the Left Arrow to undo the last selection action.
To select multiple atoms at once, use Control, Shift, and left click.
To select a broader region of the protein, keep the
Control button pressed down and use a left mouse drag to reveal a rectangle.
Upon releasing the mouse, everything within the rectangle becomes selected.
Pressing the Control button and clicking outside of the structure deselects the selected region.
Chimera's command line is readily accessible under the Favorites menu.
Now we can use the command line to perform selections within the structure.
Unsurprisingly, the key word for these commands is "select". Let's say you wanted to select a
particular range of residue positions within the structure. To do this, you would type into
the command line: select, colon, and the desired residue position range. Upon hitting Enter, these
positions are highlighted in green. If you wanted to limit the selection to a particular chain, you
would type a period followed by the desired chain code. Now the selection only applies to chain A.
To select a specific residue within a chain, the format is the same as before,
except the residue range is replaced with a single position. To select the
same residue position across a number of chains, simply add a chain range as shown.
Research has shown that the most common type of sickle cell disease-causing mutation
is a mutation from glutamic acid to valine at position 6 of the hemoglobin beta chain,
chain H. To locate this position, we can select by Sequence. Upon selecting chain H,
we are greeted with the entire amino acid sequence of that chain. Hovering over each
of these letters reveals the position ID label at the bottom of the window. In this
way we eventually come to valine 6. To select this residue, click and drag over its letter.
Notice the residue highlighted in the graphics window. Now under Actions, Atoms and Bonds,
we can show the side chain; and then we can focus in on the residue.
Once you have obtained a clear view of the residue, you may want to label it.
To do this, go to Actions, Label, Residue, and choose Name + Specifier.
This label provides the three letter code of the amino acid, its number, and its chain. You
can adjust label parameters such as font size by again going to Actions, Label and Options. The
label comes in small, so it's a good idea to set the font size to something larger.
If you would like the label to contrast with the surrounding protein, you can go to Actions,
Color, and under All Options, selectively apply the coloring to Residue Labels.
Then you can choose a color that provides better contrast.