Getting Started Tutorial - Menu Version

Many operations within Chimera can be accomplished in multiple ways. For example, colors and molecular representations can be changed by using the Actions menu or by typing commands into the Command Line. In general, using the menus involves more steps, but does not require one to remember commands and their syntax.

In this tutorial, many of the operations performed with commands in the Getting Started Tutorial - Command Version are carried out using the menus instead. It is useful but not necessary to go through both versions.

To follow along, you will first need to download the PDB files 1zik.pdb and 6bna.pdb into your working directory. (The same files are used in the Command Version.)

Menus, Part 1 - Manipulation, Selection, and Chains

On Windows/Mac, click the chimera icon; on UNIX, start Chimera from the system prompt:

unix: chimera

A basic Chimera window should appear after a few seconds. Scaling and clipping operations can be performed with the Side View. There are several ways to start this tool; one is to choose Tools... Viewing Parameters... Side View from the menu. Each window or tool can be moved to a convenient location by placing the cursor on its top bar and dragging with the left or middle mouse button. If you like, resize the main Chimera window by placing the cursor on any corner and dragging with the left mouse button.

Now open a structure. Choose the menu item File... Open. From the resulting dialog, choose and open the previously downloaded file 1zik.pdb (the File type should be set to PDB). The structure will appear in the main graphics window, and a tiny version is shown in the Side View. The structure is a leucine zipper formed by two peptides. Within the Side View, try moving the eye position (the small square; scales the view) and the clipping plane positions (vertical lines) with the left mouse button. The Side View will renormalize itself after movements, so that the eye or clipping plane positions may appear to "bounce back" after you have adjusted them; however, your adjustments have been applied to the main display.

Simplify the display:

Actions... Atoms/Bonds... hide
Actions... Atoms/Bonds... chain trace only
This shows only the atoms named CA (alpha-carbons) and connects them in the same way that the residues are connected. Try manipulating the structures in the main graphics window with the mouse. By default, the left mouse button controls rotation and the middle mouse button controls XY translation. Continue moving and scaling the structures with the mouse in the graphics window and the Side View as desired throughout the tutorial. Next, thicken the lines:
Actions... Atoms/Bonds... wire width... 3

In combination with the Ctrl key, the mouse buttons have additional functions; by default, picking from the screen (a type of selection) is done by clicking on the atom or bond of interest with the left mouse button while holding down the Ctrl key. To add to an existing selection, also hold down the Shift key. The selection is highlighted in green. Try picking two alpha-carbons, one from each peptide (Ctrl-Shift-leftbutton). Remember that the Shift key is needed to select both atoms; otherwise, only the most recent selection will be retained.

The Actions menu applies to whatever is selected. When nothing is selected, the Actions menu applies to everything.

Label the atoms you have selected, first by atom name and then by residue name and number:

Actions... Label... name
Actions... Label... off
Actions... Label... residue... name + specifier
Each residue label is of the form:
res_name res_number.chain
It is now evident that one peptide is chain A, and the other is chain B. To deselect the atoms, pick in a region of the graphics window away from any atoms or use the menu item Select... Clear Selection. Undisplay the residue labels:
Actions... Label... residue... off
Color the two chains different colors:
Select... Chain... A
Actions... Color... cyan
Repeat the process to color chain B yellow. Another way to select an entire chain is to pick an atom or bond in the chain and then hit the up arrow key twice, once to expand the selection to the entire residue and another time to expand it to the entire chain.

There is actually another "chain" in this model, not currently displayed: water. This chain ID was assigned automatically when the structure was read in.

Select... Chain... water
Actions... Atoms/Bonds... show
Select... Clear Selection
Alternatively, the water could have been selected using Select... Structure... solvent or Select... Residue... name... HOH.

To display all atoms of the A chain only:

Actions... Atoms/Bonds... hide
Select... Chain... A
Actions... Atoms/Bonds... show
Then to show the backbone only,
Actions... Atoms/Bonds... backbone only
Only the A chain's backbone is displayed because the A chain was selected when the action was performed.
Select... Clear Selection
Actions... Atoms/Bonds... show
Actions... Color... by element
displays all the atoms and colors them according to element.

A checkbox in the Active column of the Model Panel (Tools... Inspectors... Model Panel; may also be in the Favorites menu) shows that the model is activated for motion; unchecking the box makes it impossible to move. Checking the box again restores the movable state. Make sure 1zik.pdb is highlighted on the left side of the Model Panel (if not, click on it) and then click close in the list of functions on the right side. Use the Close button at the bottom to close the Model Panel. Go on to Part 2 below, OR terminate the Chimera session. A Chimera session may be ended using File... Quit.

Menus, Part 2 - Molecular Representations and Surfaces

With Chimera started and the Side View opened as described at the beginning of Part 1, choose the menu item File... Open. From the resulting dialog, choose and open the previously downloaded file 6bna.pdb (the File type should be set to PDB). It contains the molecule netropsin bound to double-helical DNA.

Color the different nucleotides different colors. For example, color the adenosine residues (adenine nucleotides) blue:

Select... Residue... name... A
Actions... Color... blue
Analogously, color cytosine nucleotides (C residues) cyan, guanine nucleotides (G residues) yellow, and thymine nucleotides (T residues) magenta. Clear the selection by using Select... Clear Selection or picking in a region of the graphics window away from any atoms.

Rotate, translate, and scale the structure as needed to get a better look (see mouse manipulation to review how this is done). Continue moving and scaling the structure as desired throughout the tutorial. There are still many white atoms, including the netropsin molecule in the minor groove of the DNA and water. Undisplay the water:

  1. pick one of the white dots (water oxygens)
  2. hit the up arrow key once to expand the selection to the entire "chain" water (when a PDB file is opened, some residues may be automatically assigned chain ID water); only one click is needed because the picked atom is equivalent to an entire residue
  3. Actions... Atoms/Bonds... hide
Next, try some different molecular representations. They can be translated, rotated, and scaled interactively. Multiple representation types can be combined with each other and with surfaces (more on surfaces below).
Select... Clear Selection (to ensure that nothing is selected; otherwise, the water is still selected, even though it is invisible)
Remember that when nothing is selected, the Actions menu applies to everything.
Actions... Ribbon... show
Actions... Ribbon... hide
Actions... Atoms/Bonds... stick
Actions... Atoms/Bonds... sphere
Change the representation of only one of the DNA strands, chain B:
Select... Chain... B
Actions... Atoms/Bonds... stick
Next, change everything to a ball-and-stick representation:
Select... Clear Selection
Actions... Atoms/Bonds... ball & stick
In this representation, pick one of the atoms in the white netropsin molecule. Label the residue by name:
Actions... Label... residue... name
The residue label may not be very close to the selected atom. Remove the residue label:
Actions... Label... residue... off
The first submenu under Label controls individual atom labels, while the second controls residue labels. Actions... Label... name would have shown the name of the atom instead of the name of the residue.

Two white atoms that are not part of netropsin are displayed. They are apparently attached to cytosines, which have been colored cyan (above). Pick the two atoms and label their residues,

Actions... Label... residue... name + specifier
showing that one DNA strand is chain A, the other strand is chain B, and each strand contains a brominated cytosine. Use Select... Clear Selection to deselect the atoms, then undisplay the residue labels:
Actions... Label... residue... off
Finally, have some fun with surfaces. There are built-in categories within structures such as main and ligand; when nothing is selected, Actions... Surface shows the surface of main. Surfaces can be translated, rotated, and scaled interactively.
Actions... Surface... show
Actions... Surface... hide
Select... Structure... ligand
Actions... Surface... show
Actions... Surface... mesh
By default, a surface has the same color as the corresponding atoms; however, surface color can be specified separately. To change the surface color only of netropsin only (which is still selected):
  1. change the coloring target: Actions... Color... surfaces
  2. Actions... Color... red
  3. restore the default coloring target: Actions... Color... all of the above
Clear the selection, change back to a solid surface, and then undisplay the surface.
Select... Clear Selection
Actions... Surface... solid
Actions... Surface... hide
As an example of a more complicated selection process, show the surface of the adenine and thymine nucleotides in chain B only:
  1. change the selection mode: Select... Selection Mode... append
  2. Select... Residue... name... A
  3. Select... Residue... name... T
  4. change the selection mode: Select... Selection Mode... intersect
  5. Select... Chain... B
  6. Actions... Surface... show
To prepare for any subsequent operations, restore the selection mode and clear the selection:
Select... Selection Mode... replace
Select... Clear Selection
The command line (Tools... Keyboard... Command Line) equivalent is much more concise, but requires some knowledge of the atom specification syntax:
Command: surf :a.b,t.b

Sometimes it is helpful to make a solid surface transparent:

Actions... Surface... transparency... 50%
Choose File... Quit from the menu to terminate the Chimera session.

meng@cgl.ucsf.edu / December 2004