Getting Started Tutorial - Menu Version

Many operations within Chimera can be accomplished in multiple ways. For example, colors and molecular representations can be changed using the Actions menu or by typing commands into the Midas Emulator. 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

Start Chimera from the UNIX prompt

unix: chimera
or, on Windows, click the chimera icon. A basic Chimera window should appear after a few seconds. Next, choose Controllers... Side View to open the Side View. 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 1zik.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... Display... off
Actions... Display... 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... Represent... line width... 3

In combination with the Ctrl key, the mouse buttons have additional functions; by default, picking from the screen 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. 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 selection is highlighted in green.

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 name and then by residue:

Actions... Label... name
Actions... Label... clear
Actions... Label... residue... both
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.
Actions... Label... residue... clear
undisplays the residue labels. It is fairly easy to specify chains. One possibility is to color the two chains different colors.
  1. pick an atom or bond in one of the chains
  2. hit the up arrow key twice to expand the selection to the entire chain (bonds/atoms expand to residues, residues expand to chains)
  3. Actions... Color... cyan
Repeat the process to color the other chain yellow. There is actually another chain in this model, not currently displayed: WATER. This chain was assigned automatically when the structure was read in. Display the water (only the oxygens are visible in the X-ray structure):
  1. open the Model Panel (Controllers... Model Panel)
  2. in the Model Panel, make sure 1zik.pdb is highlighted on the left side (if not, click on it) and then click select chain(s)... on the right side
  3. in the Select Chains widget, click the checkbox marked water, then Apply (so that the widget will remain open)
  4. Actions... Display... on
  5. Select... Clear Selection
To display all atoms of the A chain only:
  1. Actions... Display... off
  2. in the Select Chains widget, deactivate the water checkbox, activate the checkbox marked A, then click OK (which also closes the widget)
  3. Actions... Display... on
Then to show the backbone only,
Actions... Display... backbone only
Only the A chain's backbone is displayed because the A chain was selected.
Select... Clear Selection
Actions... Display... on
Actions... Color... by element
displays all the atoms and colors them according to element.

A checkbox in the Active column of the Model Panel (use Controllers... Model Panel to reinvoke it if it has disappeared) 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. The Close button at the bottom closes 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 6bna.pdb. It contains the molecule netropsin bound to double-helical DNA. 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.

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

  1. Select... Chemistry... residue type... A
  2. Actions... Color... blue
Analogously, color cytosine nucleotides (C residues) cyan, guanine nucleotides (G residues) yellow, and thymine nucleotides (T residues) magenta.

There are still many white atoms, including netropsin 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 to chain HET or WATER); only one click is needed because the picked atom is equivalent to an entire residue
  3. Actions... Display... off
Next, try some alternate representations. Note that they can be translated, rotated, and scaled interactively. Multiple representation types can be combined with each other and with surfaces (more on surfaces below). When nothing is selected, the Actions menu applies to everything.
Select... Clear Selection (to ensure that nothing is selected; otherwise, the water is still selected, even though it is invisible)
Actions... Represent... ribbon... flat
Actions... Represent... ribbon... none
Actions... Represent... stick
Actions... Represent... sphere
Change the representation of only one of the DNA strands, chain B:
  1. open the Model Panel (Controllers... Model Panel)
  2. in the Model Panel, make sure 6bna.pdb is highlighted on the left side (if not, click on it) and then click select chain(s)... on the right side
  3. in the Select Chains widget, click the checkbox marked B, then OK
  4. Actions... Represent... stick
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.

Next, change everything to a ball-and-stick representation:

Select... Clear Selection (to ensure nothing is selected)
Actions... Represent... ball & stick
In this representation, pick one of the atoms in the white netropsin molecule. Label the residue by residue name:
Actions... Label... residue... name
The label may be hard to see, depending on the size and orientation of the model (this behavior should improve in later versions). Try making the molecule smaller and/or rotating it until the residue name NT is visible. Remove the label:
Actions... Label... residue... clear
Note that the first submenu under Label controls individual atom labels rather than residue labels. If Actions... Label... name had been used, the name of the atom would have been shown instead of the name of the residue. Other than the white netropsin molecule, there are two additional white atoms. They are apparently attached to cytosines, which have been colored cyan (above). Pick and then label these two atoms,
Actions... Label... residue... both
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 and then undisplay the labels.
Actions... Label... residue... clear
Finally, have some fun with surfaces; see the surface manual page for a discussion of the built-in surfacing categories main and ligand. Surfaces can be translated, rotated, and scaled interactively.
Actions... Surface... main
Actions... Surface... clear
Actions... Surface... ligand
Actions... Surface... style... 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:
  1. Select... Chemistry... residue type... NT
  2. change the coloring target: Actions... Color... applies to... surfaces only
  3. Actions... Color... red
  4. restore the default coloring target: Actions... Color... applies to... default
Another way to select the entire netropsin residue is to undisplay (clear) the surface, pick an atom or bond in netropsin, and hit the up arrow key once to expand the selection to the entire residue. A surface obstructs underlying atoms from being picked.

Clear the selection, change back to a solid surface, and then undisplay the surface.

Select... Clear Selection
Actions... Surface... style... solid
Actions... Surface... clear
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... Chemistry... residue type... A
  3. Select... Chemistry... residue type... T
  4. change the selection mode: Select... Selection Mode... intersect
  5. open the Model Panel (Controllers... Model Panel)
  6. in the Model Panel, make sure 6bna.pdb is highlighted on the left side (if not, click on it) and then click select chain(s)... on the right side
  7. in the Select Chains widget, click the checkbox marked B, then OK
  8. Actions... Surface... main
  9. restore the default selection mode: Select... Selection Mode... replace
The command line equivalent is much more concise, but requires some knowledge of the atom specification syntax:
Command: surf :a.b,t.b

Choose File... Quit from the menu to terminate the Chimera session.

meng@cgl.ucsf.edu / October 2002