UCSF Chimera - Getting Started

Getting started

On Linux run the executable "chimera" in the bin directory of your Chimera installation. If Chimera is installed in /usr/local/chimera, then you run /usr/local/chimera/bin/chimera from a shell.

On Windows start Chimera by double clicking the Chimera icon in the directory called bin in your Chimera installation. If Chimera is installed in \Program Files then the executable will be found in directory \Program Files\Chimera\bin. A Chimera icon will also be put on your desktop by default.

On Mac start the Apple X server found in /Applications/Utilities/X11. Then double click the Chimera application to start. The X server is not installed in Mac OS 10.3 by default and if you do not have it you can download it from Apple. It is necessary for running Chimera on the Mac.

Opening a structure

A basic Chimera window should appear after a few seconds. Chimera provides a number of tools and dialogs that can all be opened on the screen at the same time. The basic Chimera window provides the main interactive workspace for displaying and manipulating molecular (or volumetric) data. The default Chimera graphics window is pretty small, so 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 if the files are local. From the resulting dialog, choose and open the previously downloaded file 1zik.pdb (the File type should be set to PDB).  If you want to fetch directly from the PDB insted, choose File→Fetch by ID,  and type 1zik in the PDB ID field.  The structure will appear in the main graphics window. The structure is a leucine zipper formed by two peptides.

Side view

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. Another is to use the Favorites menu, which is a useful place to store often used commands. By default, Side View, is initially in the Favorites menu. Once the Side View is open, you will be able to see a tiny version of the structure present in the main Chimera window.

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.

Basic manipulation

Actions Menu Items

Menu Item	Description
Color	Colors selected objects. Color target can be limited to object types indicated by the radio buttons
Label	Labels selected atoms. residue submenu provides options for residue labeling
Focus	Focuses the view on the selected atom(s), zooming and translating if necessary.
Atoms/Bonds	Controls the display and representation of atoms and bonds.
Ribbons	Controls the display and representation of secondary structure using "ribbons".
Surface	Controls the display and representation of molecular surfaces.
Target	Restricts target of the action to certain selected or unselected object types.
Inspect	Launches the Selection Inspector.
Write	Writes the currently selected objects to a file.

Selection/Action

You can now use some menu commands to simplify the display. In general, Chimera Actions act on the current Selection. If nothing is explicitly selected (see Selection section below), then actions will act on everything. The Actions menu can now be used on our model. Explore the Actions menu to see what kinds of functions it provides. As you can see, the Actions menu provides access to some general actions such as Color and Label and some actions that are specific to the type of the underlying representation such as Atoms/Bonds and Surface. The table at the right describes these menu items in more detail. We will use some of these commands later in the tutorial.

To display only the main chain, use the two actions: Actions→Atoms/Bonds→hide to undisplay the model followed by Actions→Atoms/Bonds→chain trace only to display only the chain trace, which shows all of the α-carbons (CA atoms in Chimera) and connects them in the same way that the residues are connected.

Using the mouse

Default Mouse Button Assignments

Mouse button	Modifier	Action
Btn1 (left button)		Rotation
Btn2 (middle button)		XY Translation
Btn3 (right button)		Scaling
Btn1	Ctrl	Selection
Btn1	Ctrl-Shift	Add to (or remove from) Selection
Btn2	Ctrl	Z Translation

Now use the mouse to manipulate the model in the main window. By default, the left mouse button controls rotations, the middle mouse button controls XY translation, and the right mouse button controls scaling. Note that the Side View window is reflecting all of the manipulations in the main window. Continue moving and scaling the structures with the mouse in the graphics window and Side View as desired throughout the tutorial.
Next, thicken the lines to make them more visible (we'll look at other representations later):
    Actions→Atoms/Bonds→wire width→3.

Selection

In combination with the control (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 α-carbons, one from each peptide. Remember that you will need to use Ctrl-Shift-Btn1 to select the second atom; otherwise, only the most recent selection will be retained.

In addition to using the mouse to select a single atom, use can also use the mouse to drag out a selection area. As before, you depress the Ctrl key and mouse button 1 (usually the left button), and sweep out an area before releasing. All atoms and bonds within that area will be selected. As before, Ctrl-Shift-Btn1 can be used to add to an existing selection, either by clicking or by dragging.

One additional keyboard feature is the use of the ↑ key to increase the scope of a selection. Chimera maintains a hierarchy of objects from atoms to residues to chains to models. If an atom is selected, the ↑ key will select the residue containing that atom. If a residue is selected, the ↑ key will select the chain containing that residue. If a chain is selected, the ↑ key will select the entire model. Similarly, the selection scope can be narrowed by using the ↓ key.

Spend some time selecting various parts of the model. The easiest way to deselect everything is to Ctrl-click in any blank space within the graphics window. Once you are done, reselect the two α-carbons from each of the chains so that we can begin to act on the selections.

Changing the display

Labels

As mentioned above, the Actions menu applies to whatever is selected. When nothing is selected, the Actions menu applies to everything.  Now, 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

Colors

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.

Displaying parts of the model

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.

Model panel

Chimera provides a number of other tools to observe the state of the model. One is the Model Panel ( Tools→Inspectors→Model Panel). A checkbox in the Active column of the Model Panel 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.

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

Molecular representations

Molecular Representations

Menu Item	Description
Action→Atoms/Bonds→wire width	Sets the width (thickness) of the lines in the wire representation
Action→Atoms/Bonds→wire	Bonds are displayed as connecting lines, atoms are displayed as dots
Action→Atoms/Bonds→stick	Similar to wire, bonds are represented as three-dimentional sticks and atoms are displayed as end-caps
Action→Atoms/Bonds→ball & stick	Atoms are displayed as small spheres, bonds are displayed as in stick
Action→Atoms/Bonds→sphere	Atoms are displayed as van der Waals spheres
Action→Ribbon→show	Display the secondary structure as a "ribbon"
Action→Ribbon→hide	Hide the "ribbon" display
Action→Ribbon→flat	Use a flat representation for the ribbon
Action→Ribbon→edged	Display the ribbon with flag edges
Action→Ribbon→round	Display the ribbon with rounded edges
Action→Surface→show	Display a molecular surface
Action→Surface→hide	Hide a molecular surface
Action→Surface→solid	Display a solid surface
Action→Surface→mesh	Display the surface as a mesh
Action→Surface→dot	Display the surface as dots
Action→Surface→transparency	Set the transparency of the surface

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

More with labels

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

Molecular surfaces

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

More fun with selection

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.

Front image how-to

Here are the steps to recreate the image at the front of the tutorial:

1. Read in 6bna.pdb
2. Set the representation to "stick":
• Actions→Atoms/Bonds→stick
3. Remove the waters:
   • Select→Chain→Water
   • Actions→Atoms/Bond→Hide
   • Select→Clear Selection
4. Color the residues:
   • Select→Residue→name→A
   • Actions→Color→blue
   • Select→Residue→name→C
   • Actions→Color→cyan
   • Select→Residue→name→G
   • Actions→Color→yellow
   • Select→Residue→name→T
   • Actions→Color→magenta
5. Add a surface to the DNA, color it gray, and make it transparent:
   • Actions→Surface→Show
   • Actions→Color→surfaces
   • Actions→Color→light gray
   • Actions→Surface→transparency→50%
6. Add a surface to the netropsin, color it red, and make it transparent:
   • Select→Structure→ligand
   • Actions→Surface→Show
   • Actions→Color→red
   • Actions→Color→all of the above
   • Actions→Surface→transparency→50%
7. Rotate and translate as desired
8. If desired, change the background to white:
• Actions→Color→background
• Actions→Color→white
• Actions→Color→all of the above
9. Save the image:
• File→Save Image

Getting started

On Linux run the executable "chimera" in the bin directory of your Chimera installation. If Chimera is installed in /usr/local/chimera, then you run /usr/local/chimera/bin/chimera from a shell.

On Windows start Chimera by double clicking the Chimera icon in the directory called bin in your Chimera installation. If Chimera is installed in \Program Files then the executable will be found in directory \Program Files\Chimera\bin. A Chimera icon will also be put on your desktop by default.

On Mac start the Apple X server found in /Applications/Utilities/X11. Then double click the Chimera application to start. The X server is not installed in Mac OS 10.3 by default and if you do not have it you can download it from Apple. It is necessary for running Chimera on the Mac.

Commands are entered into the Command Line and scaling and clipping operations can be performed with the Side View. There are several ways to start each of these tools; one is to choose Tools→Keyboard→Command Line and Tools→Viewing Parameters→Side View from the menu.

Now open the previously downloaded structure:

Command: open 1zik.pdb

If the file is not in the working directory, use File→Open instead, as shown in Part 2. 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.

Basic manipulation

Command/Target

You can now use some menu commands to simplify the display. In general, a Chimera command consists of the command, one or more arguments, and an optional target. If no target is specified, the command operates on the entire model. This is different from the Menu interface, in which Actions operate on the current Selection. One of the built-in targets provided in the Chimera Command Tool is selected, sel, or picked which applies the command to the current selection.

To simplify the display:

Command: chain @ca

This command shows only the atoms named CA (α-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:

Command: linewidth 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 α-carbons, one from each peptide (Ctrl-Shift-Btn1). Remember that the Shift key is needed to select both atoms; otherwise, only the most recent selection will be retained.

Label the atoms you have selected:

Command: label sel

The label command shows atom information (atom name, by default). Undisplay the atom labels, then show labels for the residues containing the selected atoms:

Command: ~label
Command: rlabel sel

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:

Command: ~rlabel

Target Specification Symbols

Symbol	Function	Usage
#	model number	# model (integer)
#.	submodel number	#.submodel (integer)
:	residue	: residue (name or number)
::	residue name	::residue (integer)
:.	chain ID	:.chain
@	atom name	@atom
@.	alternate location ID	@.alt_loc
-	range	specified a range of models, submodels, or residues
,	name separator	separates models or residues, ranges of models or residues, or names of atoms
*	whole wildcard	matches whole atom or residue names, e.g., :*@CA specifies the α-carbons of all residues
=	partial wildcard	matches partial atom or ressidue names, e.g., @C= specifies all atoms with names beginning with C
?	single-character wildcard	used for atom and residue names only, e.g., :G?? selects all residues with three-letter names beginning with G
;	command separator	separates multiple commands on a single line
z<	zone specifier	z<zone or zr<zone spcifies all residues within zone angstroms of the indicated atoms, and za<zone specifies all atoms (rather than entire residues) within zone angstromgs of the indicated atoms. Using > instead of < gives the complement.
&	intersection	intersection of specified sets
|	union	union of specified sets
~	negation	negation of specified set (when space-delimited)

Chain Targets

It is fairly easy to specify chains. Chain targets are designated by a :, followed by a ., followed by the chain name. Color the two chains different colors:

Command: color cyan :.a
Command: color yellow :.b

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

Command: disp :.water

displays the water (only the oxygens are visible in the X-ray structure);

Command: show :.a

gets rid of everything except the A chain, but displays all of its atoms;

Command: chain :.a@n,ca,c

shows the backbone of the A chain only. If the chain specification ":.a" had been omitted, then the backbones of both chains would have been displayed.

Command: disp
Command: color byelement

displays all the atoms and colors them according to element.

The Command Line also shows which models are activated for motion: below the command line, 0 should be in bold and the small box next to it highlighted. Clicking the box turns off the highlighting and makes it impossible to move the molecule in model 0. Clicking the box again restores the movable state.

Command: close 0

closes the model. Go on to Part 2 below, OR terminate the Chimera session. A Chimera session may be ended using the following command:

Command: stop

Setting Up

With Chimera started and the Command Line and 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. (Files can also be opened from the Command Line, as shown in Part 1.)

Color the different nucleotides different colors, specifying them by residue name:

Command: color blue :a
Command: color magenta :t
Command: color yellow :g
Command: color cyan :c

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:

Command: ~disp :.water
-OR- (these are equivalent)
Command: ~disp solvent

Molecular Representations

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).

Command: ribbon
Command: ~ribbon
Command: represent stick
Command: repr sphere
Command: rep stick :.b

The latter command changes only chain B to the stick representation, with the rest remaining in the sphere representation.

Note that commands (but not their keyword arguments) can be truncated to unique identifiers. For example, the command represent can be shortened to repr or rep but not re (because other commands also start with re), whereas the keywords stick, sphere, etc. cannot be truncated.

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

Command: repr bs

In this representation, pick one of the atoms in the white netropsin molecule. Label the residue,

Command: rlabel picked

showing that it is named NT and is part of chain HET (assigned automatically when the structure was read in). The residue label may not be very close to the selected atom. Remove the residue label:

Command: ~rlabel

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,

Command: rla picked

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:

Command: ~rla

Surfaces

Finally, have some fun with the surface command. There are built-in categories within structures such as main and ligand; when nothing is specified, surface shows the surface of main. Surfaces can be translated, rotated, and scaled interactively.

Command: surface
Command: ~surface
Command: surface ligand

-OR- (these are all equivalent)
Command: surface :nt
-OR-
Command: surface ::nt
-OR-
Command: surface :.het

Command: surfrepr mesh
Command: surf :g,c
Command: ~surf
Command: surf :a.b,t.b
Command: surf :a,t
Command: surf ligand

By default, a surface has the same color as the corresponding atoms; however, surface color can be specified separately:

Command: color red,s ligand
Command: ~surf ligand
Command: color green,s :t
Command: surfrepr solid

Sometimes it is helpful to make a solid surface transparent. One way to do this is to define a transparent color and then use the new color in a command:

Command: colordef tpink 1. .5 .7 .4
Command: color tpink,s

The numbers in the colordef command refer to red, green, blue, and opacity components, respectively.

Use the command stop to terminate the Chimera session.