UCSF Chimera - Getting Started

← Getting started

Start Chimera by clicking or doubleclicking the Chimera icon (depending on its location). Typically, this icon will be present on the desktop. The Chimera executable can also be run from its installation location.

A splash screen will appear, to be replaced in a few seconds by the main Chimera window containing either the graphics display or the Rapid Access list of recently used files (it doesn't matter which, since opening a structure will automatically switch the display to the graphics window). If you like, enlarge the window by clicking and dragging its lower right corner. The window can also be moved by clicking its top bar and dragging.

Side View

Show the Side View for interactive scaling and clipping (menu: Tools→Viewing Controls→Side View). By default, the Side View is also listed in the Favorites menu.

It shows a tiny version of the structure. Try moving the eye position (the small square) and the clipping planes (vertical lines) by clicking and dragging 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,” but your adjustments have been applied.

← 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	Picking (selection)
Btn1	Ctrl-Shift	Addition to (removal from) selection

Try manipulating the structure in the main window with the mouse. By default:

• the left mouse button controls rotation
• the middle mouse button controls XY translation (panning)
• the right mouse button performs scaling (zooming)

If you are using a touchpad or single-button mouse, modifier keys allow emulating the middle and right mouse buttons. These are option and command () on Mac keyboards. Multitouch gestures on a Mac touchpad are enabled by default, but can be turned off in the preferences (menu: Favorites→Preferences, category Mouse). Continue moving and scaling the structure with the mouse in the graphics window and Side View as desired throughout the tutorial.

When the mouse focus is in the graphics window (you may need to click into it if you have been interacting with a different window), hovering the mouse cursor over an atom or bond without clicking any buttons will show identifying information in a pop-up “balloon.” The balloon will disappear when the cursor is moved away. For an atom, the balloon information is of the form:

    res-name  res-num.chain  atom-name

You can see from the balloons that this structure contains two peptide chains, A and B, and water (HOH residues), also with chain identifiers A and B.

Selection with the mouse

In combination with modifier keys, the mouse buttons have additional functions. By default, picking from the screen (a type of selection) is done by Ctrl-clicking an atom or bond with the left mouse button, Btn1. You can also drag out a selection area with Ctrl-Btn1 (sweep out an area before releasing). Shift-Ctrl-Btn1 adds to or toggles an existing selection. The selection is outlined in green, and placing the mouse cursor over the green magnifying glass icon near the bottom right corner of the window reports what is selected in a pop-up “balloon.”

The arrow keys can be used to broaden (↑), narrow (↓), or invert (→) a selection. The hierarchy for broadening and narrowing a selection could include (depending on the initial selection): atom/bond, residue, protein secondary structure element, bonded set of atoms, all atoms with the same chain ID, entire model. When a selection is inverted, the selected atoms become deselected and vice versa.

Spend some time selecting various parts of the structure. An easy way to clear the selection (deselect everything) is to use Ctrl-Btn1 in any blank space in the graphics window.

Actions Menu Items

Menu Item	Description
Atoms/Bonds	Controls the display and representation of atoms and bonds.
Ribbon	Controls the display and representation of ribbons.
Surface	Controls the display and representation of molecular surfaces.
Color	Colors selected objects. Color target can be limited to object types in the all options dialog.
Label	Labels selected atoms. The residue submenu labels residues containing the selected atoms.
Focus	Focuses the view on the selected atom(s), zooming and translating if necessary.
Set Pivot	Sets the center of rotation based on the selected atom(s) without adjusting the view.
Inspect	Launches the Selection Inspector; same as clicking .
Write List	Writes a list of the currently selected objects to a parsable text file.
Write PDB	Writes the coordinates of the currently selected atoms to a PDB file.

← Selection/Action

In general, operations performed with the Chimera Actions menu apply to the current selection. Selections can be made in many ways, including with the Select menu or with the mouse (as described above). When nothing is selected, the Actions menu applies to everything.

The following will color all residues named LYS hot pink.

    Select→Residue→LYS
    Actions→Color→hot pink

The selection is highlighted in green, and the magnifying glass icon near the bottom right corner of the window is also green, indicating that something is selected. Clearing the selection (deselecting) beforehand will color everything:

    Select→Clear Selection
    Actions→Color→hot pink

Select menu choices also include chain ID, element, and many other categories of atoms and residues. (More complicated selections can be built up by intersecting some of these choices, as shown near the end of Part 2.)

    Select→Chain→B
    Actions→Color→cyan
    Actions→Ribbon→hide
    Select→Structure→solvent
    Actions→Atoms/Bonds→hide
    Select→Chemistry→element→N
    Actions→Atoms/Bonds→sphere
    Select→Clear Selection
    Actions→Atoms/Bonds→stick

One way to select specific residues or ranges of residues is in the Sequence tool (menu Favorites→Sequence, show sequence for chain A). When the sequence window has mouse focus, placing the cursor over a residue symbol in the sequence shows information for the corresponding structure residue at the bottom of the window. Click-drag a box within the sequence window to select one or more residues (as opposed to simply clicking within the light yellow box, which will select the entire helix), then hide their atoms:

    Actions→Atoms/Bonds→hide

Quit from the sequence window and display all protein atoms again:

    Select→Structure→protein
    Actions→Atoms/Bonds→show

Coloring can be limited to only certain representations, such as atoms only (not ribbons, surfaces, etc.):

    Select→Residue→GLU
    Actions→Color→all options

In the resulting Color Actions dialog:

1. choose to Show all colors (lower right)
2. change the Coloring applies to (target) setting to atoms/bonds
3. click to choose any color

Notice that only the atoms/bonds of the selected residues and not their ribbon segments change color. Clear the selection (main menu Select→Clear Selection), then in the Color Actions dialog:

1. change the coloring target back to all of the above
2. click to choose tan (colors are listed alphabetically in the all-colors section)
3. click Close to dismiss the dialog

Restore heteroatom color-coding:

    Actions→Color→by heteroatom

Coloring by heteroatom is useful for showing functional groups, yet keeping different models distinguishable by their different carbon colors.

Try picking two atoms in different residues (Ctrl-click the first, Shift-Ctrl-click the second). Show residue labels for the atoms you have selected:

    Actions→Label→residue→name + specifier

(Actions→Label→name would show the atom names instead.) These 3D labels move along with structures and are mainly for interactive use. For figures and movies, 2D Labels are recommended instead.

Promote the selection to the entire residues with the keyboard up arrow ↑ or the following:

    Select→Broaden

Show only the selected atoms:

    Actions→Atoms/Bonds→show only

Clear the selection by Ctrl-clicking in empty space, as if picking “nothing.”

Turn off residue labels, hide ribbon, display all atoms, and color by element:

    Actions→Label→residue→off
    Actions→Ribbon→hide
    Actions→Atoms/Bonds→show
    Actions→Color→by element

The by element coloring is the same as by heteroatom except it also color-codes carbons (gray).

← Models and model status

Generally, each file of coordinates opened in Chimera becomes a model with an associated model ID number. Models are assigned successive numbers starting with 0. The Model Panel lists the current models and enables many operations upon them. Open this tool with Tools→General Controls→Model Panel.

The columns on the left side of the Model Panel show:

• model ID number
• model color
• A(ctive) - whether activated for motion
• S(hown) - whether display-enabled
• model name

Try toggling the checkboxes to see what happens; a model that is not activated for motion cannot be rotated or translated interactively. In the list of functions on the right side of the Model Panel (not the button at the bottom), click close to remove model 1zik. Use the Close button at the bottom to close the Model Panel.

Go on to Part 2 below, or exit from Chimera with File→Quit.

With Chimera started as described at the beginning of Part 1, open a different structure. Choose File→Fetch by ID from the menu and enter 1d86 as the ID of the structure to fetch from the PDB. The structure contains the molecule netropsin bound to double-helical DNA, initially shown with ribbons and stylized representations of the nucleic acid sugars and bases.

Rotate, translate, and scale the structure as needed to get a better look (see Using the mouse to review how this is done). Continue moving and scaling the structure as desired throughout the tutorial.

A preset is a predefined combination of display settings. Use the “all atoms” preset, which will show the DNA as wire and netropsin as spheres:

    Presets→Interactive 2 (all atoms)

Color carbons white, then undisplay the water:

    Select→Chemistry→element→C
    Actions→Color→white
    Select→Structure→solvent
    Actions→Atoms/Bonds→hide

Remember that hiding atoms does not deselect them; they remain selected, as indicated by the green magnifying glass icon near the bottom right of the window, until the selection is cleared or replaced with a new selection.

Residue names can be identified by looking in the Select→Residue menu or by hovering the cursor over an atom or bond to see information in a pop-up “balloon.” Color the different nucleotides different colors, for example:

    Select→Residue→DA
    Actions→Color→blue

Analogously, color DC residues cyan, DG residues yellow, and DT residues magenta. Clear the selection with Select→Clear Selection or Ctrl-click in empty space.

← Representations

Next, try some different display styles, or representations.

    Actions→Atoms/Bonds→sphere
    Select→Chain→A
    Actions→Atoms/Bonds→ball & stick
    Select→Clear Selection
    Actions→Atoms/Bonds→stick

Showing ribbon automatically hides the mainchain (backbone) atoms.

    Actions→Ribbon→show
    Actions→Ribbon→edged
    Actions→Ribbon→rounded

DNA can be shown with special nucleotide objects. We will show “lollipops,” boxes, and a ladder.

    Actions→Atoms/Bonds→nucleotide objects→settings

In the resulting Nucleotides dialog:

1. set Show side (sugar/base) as to tube/slab
2. set Show base orientation to false
3. click Slab Style tab, set slab style to skinny
4. click Slab Options tab, set Slab object to ellipsoid
5. click Apply; these are the “lollipops”

Nucleotide settings can be applied to just the selected residues (not necessarily all of the DNA). One way to select specific residues is in the Sequence tool:

    Favorites→Sequence

Show the sequence of chain A and select one or a few residues in the sequence window with the mouse; this selects the corresponding part of the structure. Quit from the sequence window. In the Nucleotides dialog (also under Tools→Depiction in the menu):

1. set Show base orientation to true
2. set Slab object to box
3. click Apply; base orientations are shown with “bumps”

Clear the selection (Select→Clear Selection), then use Nucleotides to show the DNA as a ladder:

1. set Show side (sugar/base) as to ladder
2. in the Ladder Options, set Rung radius to 0.3 Å
3. click OK (which will also dismiss the dialog)

To return to more general display styles, turn off the nucleotide objects:

    Actions→Atoms/Bonds→nucleotide objects→off

Hide the ribbons and show everything as ball-and-stick:

    Actions→Ribbon→hide
    Actions→Atoms/Bonds→ball & stick

← Surfaces

Finally, have some fun with molecular surfaces. There are built-in categories within structures such as main and ligand; when nothing is selected, Actions→Surface→show displays the surface of main.

    Actions→Surface→show
    Actions→Surface→hide
    Select→Structure→ligand
    Actions→Surface→show
    Actions→Surface→mesh

Surface color can be specified separately from the colors of the underlying atoms. The ligand surface is tan and white because the original model color (tan) is used for surfaces of atoms not explicitly recolored by the user, and above, only the carbon atoms were changed to white. With the ligand still selected, choose Actions→Color→all options... to open the Color Actions dialog. In that dialog:

1. change the Coloring applies to (target) setting to surfaces
2. click red
3. click Close (which will automatically reset the coloring target back to 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 deoxynucleotides in chain B only:

1. change the selection mode: Select→Selection Mode→append
2. Select→Residue→DA
3. Select→Residue→DT
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 (or Ctrl-click in empty space)

The command-line (Tools→General Controls→Command Line) equivalent is much more concise, but requires some knowledge of the atom specification syntax:

Command: surf :da.b,dt.b

Sometimes it is helpful to make a surface transparent:

    Actions→Surface→transparency→50%

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

← Front image how-to (menu)

How to recreate the image at the front of the tutorial using the menu (see commands):

1. Choose File→Fetch by ID and fetch PDB entry 1d86
2. Use the all atoms preset:
• Presets→Interactive 2 (all atoms)
3. Set the display style to stick:
• Actions→Atoms/Bonds→stick
4. Delete the waters:
   • Select→Structure→solvent
   • Actions→Atoms/Bonds→delete
5. Color the residues:
   • Select→Residue→DA
   • Actions→Color→blue
   • Select→Residue→DC
   • Actions→Color→cyan
   • Select→Residue→DG
   • Actions→Color→yellow
   • Select→Residue→DT
   • Actions→Color→magenta
   • Select→Residue→NT
   • Actions→Color→white
6. Broaden the selection to the whole chain and then to the whole model (both ligand and main), show surfaces, make them transparent:
   • Select→Broaden
   • Select→Broaden
   • Actions→Surface→Show
   • Actions→Surface→transparency→40%
7. Set coloring to surfaces only, make them light gray:
   • choose Actions→Color→all options... to show the Color Actions dialog, and in that dialog:
     • change the Coloring applies to (target) setting to surfaces
     • click light gray (keep the dialog open)
8. Select just netropsin again, make just its surface red:
   • Select→Residue→NT
   • in the Color Actions dialog:
   • click red (keep the dialog open)
   • Select→Clear Selection
9. Set coloring to background only, make it white:
   • in the Color Actions dialog:
     • change the coloring target to background
     • click white
     • click Close (which will automatically reset the coloring target back to all of the above)
10. Adjust the view as desired
11. Save the image:
• File→Save Image

← Getting started

Start Chimera by clicking or doubleclicking the Chimera icon (depending on its location). Typically, this icon will be present on the desktop. The Chimera executable can also be run from its installation location.

A splash screen will appear, to be replaced in a few seconds by the main Chimera window containing either the graphics display or the Rapid Access list of recently used files (it doesn't matter which, since opening a structure will automatically switch the display to the graphics window). If you like, enlarge the window by clicking and dragging its lower right corner. The window can also be moved by clicking its top bar and dragging.

Show the Command Line with Tools→General Controls→Command Line. By default, the Command Line is also listed in the Favorites menu.

Opening a structure

Now open a structure. To fetch the structure of entry 1zik from the Protein Data Bank (PDB), use the command:

Command: open 1zik

The structure will appear in the graphics window; it is a leucine zipper formed by two peptides.

The default initial display is ribbons. To also display atoms:

Command: display

This shows all of the atoms and bonds in the structure, except that those in the peptide backbone are suppressed by the ribbon display. How to indicate specific parts of a structure for display, coloring, etc. is discussed below. Initially, heteroatoms (atoms other than carbon) are color-coded by element: oxygens red, nitrogens blue, etc. The carbons retain the model color, in this case tan.

Hide ribbons to reveal the backbone atoms, then show ribbons again:

Command: ~ribbon
Command: ribbon

Many commands have “~” versions that perform the opposite function.

Side View

Show the Side View for interactive scaling and clipping:

Command: start Side View

By default, the Side View can also be started from the Favorites menu.

It shows a tiny version of the structure. Try moving the eye position (the small square) and the clipping planes (vertical lines) by clicking and dragging 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,” but your adjustments have been applied.

← Using the mouse

Try manipulating the structure in the main window with the mouse. By default:

• the left mouse button Btn1 controls rotation
• the middle mouse button Btn2 controls XY translation (panning)
• the right mouse button Btn3 performs scaling (zooming)

If you are using a touchpad or single-button mouse, modifier keys allow emulating the middle and right mouse buttons. These are option and command () on Mac keyboards. Multitouch gestures on a Mac touchpad are enabled by default, but can be turned off in the preferences (menu: Favorites→Preferences, category Mouse). Continue moving and scaling the structure with the mouse in the graphics window and Side View as desired throughout the tutorial.

When the mouse focus is in the graphics window (you may need to click into it if you have been interacting with a different window), hovering the mouse cursor over an atom or bond without clicking any buttons will show identifying information in a pop-up “balloon.” The balloon will disappear when the cursor is moved away. For an atom, the balloon information is of the form:

    res-name  res-num.chain   atom-name

You can see from the balloons that this structure contains two peptide chains, A and B, and water (HOH residues), also with chain identifiers A and B.

Selection with the mouse

In combination with modifier keys, the mouse buttons have additional functions. By default, picking from the screen (a type of selection) is done by Ctrl-clicking an atom or bond with the left mouse button, Btn1. Additionally pressing Shift adds to or toggles an existing selection. The selection is outlined in green, and placing the mouse cursor over the green magnifying glass icon near the bottom right corner of the window reports what is selected in a pop-up “balloon.”

The arrow keys can be used to broaden (↑), narrow (↓), or invert (→) a selection. The hierarchy for broadening and narrowing a selection could include (depending on the initial selection): atom/bond, residue, protein secondary structure element, bonded set of atoms, all atoms with the same chain ID, entire model. When a selection is inverted, the selected atoms become deselected and vice versa.

Spend some time selecting various parts of the structure. An easy way to clear the selection (deselect everything) is to use Ctrl-Btn1 in any blank space in the graphics window.

← Command/Target

A Chimera command may include arguments and a target (or atom specification). For example, in the following color command,

Command: color hot pink :lys

hot pink is an argument that specifies a color name, and :lys specifies that the target is all residues named LYS.

If no target is specified, the command acts on all applicable items. For example, the following makes everything hot pink:

Command: color hot pink

A basic specification may contain residue names, residue numbers, chain identifiers, and/or atom names (see the table of symbols, right). Note also that commands can be truncated to unique strings.

Command: color yellow :20-22
Command: col gray :20-22.a
Command: ~disp :hoh.a
Command: col cyan :.b
Command: ~ribbon :.b
Command: ~disp :5-10.a,15-20.b
Command: represent sphere @cd2
Command: rep stick
Command: col red :leu.b@ca

The Chimera Quick Reference Guide lists all of the commands and gives some examples of atom specification. It can be accessed by choosing Help→Tutorials from the Chimera menu and clicking the “Chimera Quick Reference Guide” link.

Many other types of specifications can be used, including element symbols and built-in classifications such as solvent:

Command: ~disp solvent
Command: color blue S
Command: disp protein

The command help can be used to show the manual page for any command:

Command: help color

As explained in the manual page, the color command also allows coloring only certain representations. For example, “,a” in the following means atoms only (not ribbons, surfaces, etc.):

Command: col gold,a :glu,lys

Restore the original coloring:

Command: col tan
Command: col byhet

Coloring by heteroatom is useful for showing functional groups, yet keeping different models distinguishable by their different carbon colors.

Try picking two atoms in different residues (Ctrl-click the first, Shift-Ctrl-click the second). Unlike the Actions menu, commands do not automatically act on the current selection. However, the current selection can be specified as the target of a command with the word selected, sel, or picked. Show residue labels for the atoms you have selected:

Command: rlabel sel

(The label command shows atom information instead.) The 3D labels from rlabel and label move along with structures and are mainly for interactive use. For figures and movies, 2D Labels are recommended instead.

The following command can be used to promote the selection to the entire residues:

Command: select up

(The keyboard up arrow ↑ also broadens a selection, but you may need to click into the graphics window first to use that approach.) Show only the selected atoms:

Command: show sel

Clear the selection by Ctrl-clicking in empty space, as if picking “nothing.”

Turn off residue labels, hide ribbon, display all atoms, and color by element:

Command: ~rlab
Command: ~ribbon
Command: disp
Command: col byelement

Coloring byelement is the same as byhet except it also color-codes carbons (gray).

← Models and model status

Generally, each file of coordinates opened in Chimera becomes a model with an associated model ID number. Models are assigned successive numbers starting with 0.

The Active models line right under the Command Line shows which models are activated for motion. Unchecking the box for 0 makes it impossible to rotate or translate model 0 interactively. Checking the box again restores the movable state. A similar row of checkboxes for toggling model display can be shown using the preferences (menu: Favorites→Preferences, category Command Line).

Remove the model:

Command: close 0

Go on to Part 2 below, OR exit from Chimera with the following command:

Command: stop

← Setup

With Chimera started and the Command Line opened as described at the beginning of Part 1, fetch the structure of entry 1d86 from the Protein Data Bank (PDB):

Command: open 1d86

The structure contains the molecule netropsin bound to double-helical DNA, initially shown with ribbons and stylized representations of the nucleic acid sugars and bases.

Rotate, translate, and scale the structure as needed to get a better look (see Using the mouse to review how this is done). Continue moving and scaling the structure as desired throughout the tutorial.

A preset is a predefined combination of display settings. Use the “all atoms” preset, which will show the DNA as wire and netropsin as spheres:

Command: preset apply int 2

Color carbons white, then undisplay the water:

Command: color white C
Command: ~disp solvent

Residue names can be identified by looking in the Select→Residue menu or by hovering the cursor over an atom or bond to see information in a pop-up “balloon.” Color the different nucleotides different colors, specifying them by residue name:

Command: color blue :da
Command: color cyan :dc
Command: color yellow :dg
Command: color magenta :dt

← Representations

Next, try some different display styles, or representations.

Command: represent sphere
Command: repr bs :.a
Command: rep stick

Notice that commands but not necessarily their keyword arguments can be truncated to unique strings. For example, the command represent can be shortened to repr or rep but not re (because other commands also start with re), whereas its keywords stick, sphere, etc. cannot be truncated. If the truncation is not unique, one of the corresponding commands will be executed, but it may not be the one intended.

Showing ribbon automatically hides the mainchain (backbone) atoms.

Command: ribbon
Command: ribrep edged
Command: ribr rounded

DNA can be shown with special nucleotide objects. We will show “lollipops,” boxes with orientation bumps, and then a ladder. You can copy and paste into the Command Line. The command-line contents can be edited, and past commands can be accessed using the up and down arrow keys or Ctrl-p (previous) and Ctrl-n (next).

Command: nuc side tube/slab shape ellipsoid orient false style skinny
Command: nuc side tube/slab shape box orient true style skinny :8-10.a
Command: nuc side ladder radius 0.3

To return to more general display styles, turn off the nucleotide objects:

Command: ~nuc

Hide the ribbons and show everything as ball-and-stick:

Command: ~ribbon
Command: rep bs

← Surfaces

Finally, have some fun with molecular surfaces. There are built-in categories within structures such as main and ligand; when nothing is specified, surface shows the surface of main.

Command: surface
Command: ~surf
Command: surf ligand
   -OR- (equivalent)
Command: surf :nt

Surface color can be specified separately from the colors of the underlying atoms. The ligand surface is tan and white because the original model color (tan) is used for surfaces of atoms not explicitly recolored by the user, and above, only the carbon atoms were changed to white. Show the ligand surface as red mesh:

Command: surfrep mesh
Command: color red,s ligand
Command: surfrep solid

Parts of a surface can be shown:

Command: ~surf
Command: surf :da,dt
Command: ~surf
Command: surf :da.b,dt.b

Sometimes it is helpful to make a surface transparent:

Command: transp 50,s

When finished, exit from Chimera:

Command: stop now

← Front image how-to (commands)

How to recreate the image at the front of the tutorial using commands (see menu approach):

1. Fetch 1d86:
   • Command: open 1d86
2. Use the all atoms preset:
   • Command: preset apply int 2
3. Set the display style to stick:
   • Command: repr stick
4. Delete the waters:
   • Command: del solvent
5. Color the residues:
   • Command: color blue :da
   • Command: color cyan :dc
   • Command: color yellow :dg
   • Command: color magenta :dt
   • Command: color white :nt
6. Show surfaces for the whole model (both ligand and main), make them transparent:
   • Command: surf #0
   • Command: surftrans 40
7. Color the main (DNA) surface light gray and the ligand (netropsin) surface red:
   • Command: color light gray,s main
   • Command: color red,s ligand
8. Change the background color to white:
   • Command: set bg_color white
9. Adjust the view as desired
10. Save the image:
    • Command: copy png file ~/Desktop/myfile.png