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, run /usr/local/chimera/bin/chimera from a shell.

On Windows, start Chimera by doubleclicking the Chimera icon in the directory called bin in your Chimera installation. If Chimera is installed in \Program Files the executable will be in the directory \Program Files\Chimera\bin. By default, a Chimera icon will also be placed on your desktop.

On Mac, start Chimera by clicking the Chimera icon or by doubleclicking the Chimera application in the Finder window.

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 does not matter which, the following instructions will work with either; the Rapid Access interface reverts to the graphics display as soon as something is opened). If you like, enlarge the main window by clicking and dragging its lower right corner. Chimera includes a number of tools and dialogs that can be present on the screen at the same time. Each Chimera window or tool can be moved to a convenient location by clicking its top bar and dragging.

Now open a structure. Choose File→Fetch by ID and type 1zik in the PDB ID field. The structure will appear in the main graphics window; it is a leucine zipper formed by two peptides.

A preset is a predefined combination of display settings. Apply interactive preset #2:

    Presets→Interactive 2 (all atoms)

This displays all atoms and color-codes atoms other than carbon by element (oxygens red, nitrogens blue, etc.); carbons are left in the initial model color, in this case tan.

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 Controls→Side View from the menu. By default, the Side View is also listed in the Favorites menu. The Side View shows a tiny version of the structure.

Within the Side View, try moving the eye position (the small square) and the clipping planes (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,” 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, and the right mouse button controls scaling. On a Mac with a one-button mouse, the middle and right buttons can be emulated by combining mouse action with the option and (apple) keys, respectively.

Continue moving and scaling the structures 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.

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 (Btn1) while holding down the Ctrl key. To add to an existing selection, also hold down the Shift key. The selection is highlighted in green, and placing the mouse cursor over the green magnifying glass icon near the bottom right corner of the window pops up a “balloon” that reports what is selected.

You can also drag out a selection area with Ctrl-Btn1 (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.

The arrow keys can be used to broaden, narrow, or invert a selection. Chimera maintains a hierarchy of objects from atoms to residues to chains to models. If an atom is selected, the ↑ key will broaden the selection to the residue containing that atom. If an entire residue is selected, the ↑ key will broaden the selection to the chain containing that residue. If a chain is selected, the ↑ key will broaden the selection to the entire model. Similarly, the selection scope can be narrowed using the ↓ key. The → key inverts the selection so that selected atoms become deselected and vice versa.

Spend some time selecting various parts of the model. An easy way to 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 indicated by the radio buttons.
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.
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 affect 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 current selection is highlighted in green in the structure(s), and the magnifying glass icon near the bottom right corner of the window is also green when a selection exists.

Changing the display

Select and hide the water (red dots):

    Select→Structure→solvent
    Actions→Atoms/Bonds→hide

Alternatively, the water could have been selected using Select→Residue→HOH. Even though the water is hidden, it is still selected.

Clear the selection and display only the chain trace:

    Select→Clear Selection
    Actions→Atoms/Bonds→backbone only→chain trace

The chain trace includes just the α-carbons (atoms named CA), connected in the same way that the residues are connected.

Try picking two α-carbons, one from each peptide (using Ctrl-Btn1 for the first, Ctrl-Shift-Btn1 for the second). 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

One peptide is chain A and the other is chain B. Clear the selection and undisplay the residue labels:

    Select→Clear Selection
    Actions→Label→residue→off

(Another way to clear a selection is to Ctrl-Btn1 click in empty space.)

Color the two chains different colors:

    Select→Chain→A
    Actions→Color→cyan

Repeat the process to color chain B yellow.

Select chain A by picking any atom or bond in the chain, then hitting the ↑ key twice, once to expand the selection to the entire residue and another time to expand it to the entire chain. Display its full backbone:

    Actions→Atoms/Bonds→backbone only→full

Display all atoms of chain A only (which is still selected):

    Actions→Atoms/Bonds→show only

Display all atoms and color them by element:

    Select→Clear Selection
    Actions→Atoms/Bonds→show
    Actions→Color→by element

The by element coloring applies to all elements including carbon (gray), whereas by heteroatom coloring (as in the preset used near the beginning of the tutorial) leaves carbons unchanged. Heteroatom-only coloring is useful for keeping different structures distinguishable by their different carbon colors.

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 shows the current models and enables many operations upon them. Open this tool with Tools→General Controls→Model Panel. By default, the Model Panel is also listed in the Favorites menu.

A checkbox in the A(ctive) 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 the line for 1zik 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 exit from Chimera with File→Quit.

With Chimera started and the Side View opened as described at the beginning of Part 1, open a different structure. Choose File→Fetch by ID and type 1d86 in the PDB ID field. The structure contains the molecule netropsin bound to double-helical DNA.

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 until the selection is cleared or replaced with a new selection.

Color the different nucleotides different colors. For example, color the adenine deoxynucleotides blue:

    Select→Residue→DA
    Actions→Color→blue

Analogously, color cytosine deoxynucleotides (DC residues) cyan, guanine deoxynucleotides (DG residues) yellow, and thymine deoxynucleotides (DT residues) magenta. Clear the selection with Select→Clear Selection or by picking in empty space.

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.

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

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 solid 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

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

On Windows, start Chimera by doubleclicking the Chimera icon in the directory called bin in your Chimera installation. If Chimera is installed in \Program Files the executable will be in the directory \Program Files\Chimera\bin. By default, a Chimera icon will also be placed on your desktop.

On Mac, start Chimera by clicking the Chimera icon or by doubleclicking the Chimera application in the Finder window.

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 does not matter which, the following instructions will work with either; the Rapid Access interface reverts to the graphics display as soon as something is opened). If you like, enlarge the main window by clicking and dragging its lower right corner. Chimera includes a number of tools and dialogs that can be present on the screen at the same time. Each Chimera window or tool can be moved to a convenient location 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 directly from the PDB, use the command:

Command: open 1zik

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

A preset is a predefined combination of display settings. Apply interactive preset #2:

Command: preset apply int 2

This displays all atoms and color-codes atoms other than carbon by element (oxygens red, nitrogens blue, etc.); carbons are left in the initial model color, in this case tan.

Side View

Show the Side View:

Command: start Side View

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

The Side View allows interactive scaling (zooming) and clipping. Within the Side View, try moving the eye position (the small square) and the clipping planes (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,” 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) button controls XY translation, and the right mouse button (Btn3) controls scaling. On a Mac with a one-button mouse, the middle and right buttons can be emulated by combining mouse action with the option and (apple) keys, respectively.

Continue moving and scaling the structures 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.

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 (Btn1) while holding down the Ctrl key. To add to an existing selection, also hold down the Shift key. The selection is highlighted in green, and placing the mouse cursor over the green magnifying glass icon near the bottom right corner of the window pops up a “balloon” that reports what is selected.

The arrow keys can be used to broaden (↑), narrow (↓), or invert (→) a selection. The hierarchy for broadening and narrowing selections contains atoms, residues, chains, and models, in that order. When a selection is inverted, the selected atoms become deselected and vice versa.

Spend some time selecting various parts of the model. An easy way to 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 the target :lys specifies all residues named LYS. (To see the built-in colors and their names, choose Actions→Color→all colors from the menu.)

If no target is specified, the command acts on all applicable items. For example,

Command: color hot pink

makes all atoms (and their labels, surfaces, etc.) hot pink.

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.

Many commands have “~” versions that perform the opposite function. For example, change the structure back to its default color:

Command: ~color

The command help can be used to show the manual page for any command. For example,

Command: help color

shows the manual page for the command color. 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.

Changing the display

Display only the atoms named CA (α-carbons):

Command: show @ca

Try picking two α-carbons, one from each peptide (using Ctrl-Btn1 for the first, Ctrl-Shift-Btn1 for the second). 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

One peptide is chain A and the other is chain B. Clear the selection and undisplay the residue labels:

Command: ~select
Command: ~rlabel

Color the two chains different colors; note that commands can be truncated to unique strings:

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

Residues and atoms can also be specified, along with or independent of chain:

Command: col orange :5-9.a,12.a,8.b
Command: col magenta :14-18
Command: disp :leu.b
Command: col green :leu.b@cb

The structure also includes water, which can be shown with:

Command: disp solvent
   -OR- (equivalent)
Command: disp :hoh

Display the full backbone of chain A:

Command: disp :.a@n,ca,c,o

Display all atoms in chain A only:

Command: show :.a

Display all atoms and color them by element:

Command: disp
Command: color byelement

The byelement coloring applies to all elements including carbon (gray), whereas byhet coloring (as in the preset used near the beginning of the tutorial) leaves carbons unchanged. Heteroatom-only coloring is useful for keeping different structures distinguishable by their different carbon colors.

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 in the Command Line tool shows which models are activated for motion. The checkbox for 0 (currently the leucine zipper) is activated. Unchecking the box makes it impossible to move model 0. Checking the box again restores the movable state.

Command: close 0

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

Command: stop

Setup

With Chimera started and the Command Line and Side View opened as described at the beginning of Part 1, open a different structure. Fetch the structure directly from the PDB:

Command: open 1d86

The structure contains the molecule netropsin bound to double-helical DNA.

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

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.

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 the 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 solid surface transparent:

Command: surftrans 50

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