Chimera Menus
The major menu headings are:
The menus are tear-off, as indicated by dashed lines;
choosing the dashed line instead of a menu entry makes the menu
an independent window that remains up until explicitly closed.
Unavailable options are grayed out.
File
-
Restore Session... bring up a dialog for
opening a previously saved
session (Python file)
- Save Session - save the current
session
in the working directory; available when the current session
has been named with Save Session As... or was started by
restoring an existing session)
- Save Session As...
bring up a dialog for
saving the current
session
to a specified name and directory location
- Close Session - clear session contents without exiting from Chimera
- Quit - exit from Chimera
Select
Selection designates items for subsequent
Actions.
When nothing is selected, Actions
apply to "all." (Note: Any of the entries in Chemistry,
Residue... amino acid category, and
Structure can also be used to specify atoms in the
Command Line.)
- Chain
[only chain IDs found in currently open structures will be listed]
- Chemistry
- element
[many entries]
- functional group
[many entries]
- IDATM type
[many entries]
- Residue
- amino acid category
[many entries]
(the existing amino acid categories can be changed and new
categories defined and listed here, using
ResProp)
[only residue names found in currently open structures will be listed,
sorted into nonstandard residues, standard nucleic acids,
and standard amino acids]
- Structure
- backbone (only applies to amino acids and/or nucleic acids)
- full - the amide backbone in peptides,
the sugar-phosphate backbone in nucleic acids
- minimal - a continuous series of bonded atoms
connecting the chain trace
atoms (-[N-CA-C]n- in peptides and
-[O5'-C5'-C4'-C3'-O3'-P]n- in nucleic acids)
- ions - ions,
using the same definition
as surface calculations
- ligand - ligand,
using the same definition
as surface calculations
- main - main,
using the same definition
as surface calculations
- nucleic acid - nucleosides, nucleotides, RNA, and DNA
- protein - amino acids, peptides, and proteins
- secondary structure (only applies to peptides/proteins;
helix and strand assignments are taken from the input structure
file or generated with ksdssp)
- helix - residues in helices
- strand - residues in strands
- turn - residues in turns according to the input file
- side chain/base
(only applies to amino acids and/or nucleic acids)
- with CA/C1'
- without CA/C1'
- solvent - solvent,
using the same definition
as surface calculations
(other categorizations can be defined and listed
in the top section of the Select menu,
using the Selector Construction Panel)
-
Sequence... find and
select a specified amino acid and/or nucleotide sequence (atoms and bonds
in any/all matching segments will be selected)
- Atom Specifier... use
atom specification syntax for selection
- By Attribute Value... open the
Select by Attribute tool to select by attribute values
-
Zone... select atoms and bonds within (or beyond)
a specified distance from the currently selected atoms, on a per-atom or
whole-residue basis
- Clear Selection - clear (deselect) the current selection
- Invert (all models) - select all currently
unselected atoms and deselect all currently selected atoms
- Invert (selected models) - in models containing selections only,
select all currently unselected atoms and deselect all currently selected atoms
- Select All - select all open models and their constituent parts
- Selection Mode (current_mode)
- control whether a new selection via the menu will be
added to, subtracted from, intersected with, or used to replace
the existing selection
- Broaden - expand the current selection up a
level in the selection cascade
- Narrow - narrow a previously broadened selection down a
level in the selection cascade
- Undo - undo the most recent selection operation
- Name Selection...
name and save the current selection
(see also the command namesel).
The selection contents are remembered, not the process by which the
selection was generated (i.e., if all oxygens in the current
structure(s) are selected, later retrieving the named selection when
different structures are open will not select their oxygens).
- Named Selections - retrieve a previously saved selection
- Construct Selector...
open the Selector Construction Panel
to define a complex selection of atoms and bonds
Actions
Which items are affected by Actions
(the targets)
depends on the current selection.
For actions under Atoms/Bonds,
Ribbon,
Surface,
Color,
Label,
Focus,
and Set Pivot:
- When nothing is selected, the action affects all applicable items:
molecule models and/or surface models,
depending on the action.
- Surface actions apply not only to selected
surface pieces, but also to the
molecular surface patches
of selected atoms.
Inspection and
file-writing actions, however,
apply only to explicit selections.
- Atoms/Bonds
(see also the commands display
and represent)
- show
- show only
- hide
- backbone only
- only applies to residues in bonded chains of amino acids or nucleic acids
- chain trace
- show only one atom per residue, CA in each amino acid and
C4' in each nucleic acid residue
(turns on auto-chaining)
- full - show only the amide backbone in peptides,
the sugar-phosphate backbone in nucleic acids
- minimal - show only a continuous series of bonded atoms
connecting the chain trace
atoms (-[N-CA-C]n- in peptides and
-[O5'-C5'-C4'-C3'-O3'-P]n- in nucleic acids)
- side chain/base
- only applies to residues in bonded chains of amino acids or nucleic acids.
Each amino acid side chain includes any side chain
atoms from CB outward, plus the atom CA (for connectivity purposes);
similarly, each nucleic acid base includes the base
plus the sugar atom to which it is bonded, usually named C1'.
- show - display side chains/bases and turn
auto-chaining on
- show only - undisplay other atoms in the chain and turn
auto-chaining off
- wire width
- always affects entire molecule models even
though the targets may be narrower
(like the command linewidth)
- wire
(wire representation)
- stick
(stick representation)
- ball & stick
(ball-and-stick representation)
- sphere
(sphere or CPK representation)
- delete - remove atoms/bonds (caution: irreversible)
like the command delete
- Ribbon
- secondary structure ribbon
(see also the commands ribbon
and ribrepr).
Ribbons are only drawn for proteins and nucleic acids.
By default, showing ribbon hides the corresponding
mainchain atoms
(but see ribbackbone).
Protein helix and strand assignments are taken from the input structure
file or generated with ksdssp.
- show
- hide
- flat
- edged
- rounded
- supersmooth
(note that additional styles can be defined and listed here, using the
Ribbon
Style Editor)
- Surface
- molecular surfaces
and surface models.
Representations (solid, mesh, and dot) always apply
to entire surface pieces
even though the targets may be narrower.
- show
- hide
- solid
- mesh
- dot
- transparency
(surfaces colored with
tcolor will not be affected)
- 0%
- 10%
- 20%
- 30%
- 40%
- 50%
- 60%
- 70%
- 80%
- 90%
- 100%
- other...
set surface transparency percentage to a typed-in value
- base color
- use transparencies included in color definitions
(rather than overriding them via this menu)
- Color
(see also the command color)
- [20 top tier colors]
The following control which level(s) in the
coloring hierarchy will be affected by a subsequent color choice.
- by heteroatom
- use a built-in
color-by-element scheme, except leaving carbon atoms unchanged;
does not affect ribbons, residue labels, background, or depth cue colors
- by element
- use a built-in
color-by-element scheme; does not affect
ribbons, residue labels, background, or depth cue colors
- from editor - open the
Color Editor
and use its current color; apply any color adjustments made in the
Color Editor until it is closed
or reassigned to a different coloring operation by
clicking a color well.
If during that time the selection is changed, any color adjustments
will be applied to the new selection.
- none - remove color assignments;
assignments at other levels in the
coloring hierarchy may become visible
- all colors - a further menu of
60 built-in colors
- Label
(see also the command label)
- off - undisplay atom labels
- name - label atoms by name
(with any alternate location ID appended)
- element - label atoms by element
- IDATM type - label atoms by
atom type
- other...
label atoms with an arbitrary string or with the values of
atom attributes:
- altLoc - alternate location identifier, if any
- bfactor - B-factor value, if any
- defaultRadius -
default VDW radius
- occupancy - occupancy value, if any
- radius - VDW radius (may have been changed by the user
from the default VDW radius)
- serialNumber - serial number in the input file
- surfaceCategory - category to which the atom has been assigned
automatically
or manually using msms cat
(or surfcat)
(newly generated numerical, boolean, or string-valued atom
attributes will also be listed)
- residue
(see also the command rlabel)
- A residue label is placed at the centroid of the displayed atoms
in the residue. When ribbon is displayed instead of
mainchain atoms,
mainchain atom positions are still used in computing the centroid.
- off - undisplay residue labels
- name - label residues by name
- 1-letter code - label standard
amino acid residues by one-letter code, other residues by name
- specifier
- label residues by specifier (residue number,
insertion code, and chain ID); see custom
residue labeling for number alone
- name + specifier - label residues by name and
specifier
- 1-letter code + specifier - label standard amino acid residues
by 1-letter code and specifier,
other residues by name and specifier
- custom...
custom-label residues
with an arbitrary string and/or other residue information such as
attributes
- Focus - focus the view on the
targets that are also displayed,
possibly including items that are
invisible
(similar to the command focus).
Focusing consists of:
- adjusting the view to include the item(s)
(similar to window)
- setting the center of rotation to the center of view
(like cofr view)
- Set Pivot
- set the center of rotation to the center of the bounding box of the
targets
(similar to the command cofr).
When nothing is selected, Set Pivot restores the default
center of rotation method,
center of models, in which the center of rotation is the
center of the bounding box of the currently
active models
(displayed portions only; may include items that are
invisible).
- Inspect -
open the Selection Inspector,
which lists what items are selected, shows their attributes, and allows
their attributes to be changed
- Write List...
bring up a dialog for saving specifications
as a parsable list. Specifications can be saved for
the selected (or unselected) atoms, bonds, pseudobonds,
residues, molecules (molecule models), or models
(non-molecule models: molecular surface, surface, VRML, and volume).
The specifications can be written in the
simple (e.g., #0 PHE 16 CD1) or
command-line specifier
(e.g., #0:16@CD1) naming style.
Clicking the Log button sends the information to the
Reply Log instead of saving a file.
- Write PDB... bring up a dialog for
saving the selection as a PDB file
Presets
A preset is a predefined combination of display settings.
Choosing an entry in the Presets menu applies its settings
and is much easier than adjusting the many settings individually.
Presets are provided for a handful of usage scenarios; of course,
many more combinations of settings are possible.
See also: the preset command, the
New Molecules preferences
- Interactive presets
are meant for interactive manipulation and
analysis. They may change what items (atoms, ribbons, surfaces) are displayed
and how they are colored.
The ribbons setup shows atomic detail for all nucleic acid residues,
and for any amino acid sidechains and other residues within 3.5 Å
of a ligand residue or metal ion.
A hydrophobicity surface shows amino acid hydrophobicity
in the Kyte-Doolittle scale
with colors ranging from
dodger blue for the most hydrophilic to white at 0.0 to
to orange red for the most hydrophobic.
Surfaces of nonpeptides (which do not have Kyte-Doolittle hydrophobicity
values) will be colored to match the underlying atoms instead.
- Publication presets
are intended for generating images for
presentation and publication. They do not change what items are displayed
or their colors, but may change their styles and the color of the background.
For example, choosing a preset with rounded ribbon or
licorice will not turn on ribbon display, but will adjust any
currently displayed ribbon segments; similarly, only the currently displayed
atoms and bonds will be shown as sticks.
Publication presets may decrease interactive performance
because finer divisions are used to depict curved objects
(molecular surfaces,
ribbons, etc.).
Individual display parameters are discussed in more detail in the
tips on preparing images.
Tools
The Tools menu contains the Chimera tools or extensions.
In general, there will be several submenus of the form
where choosing an individual tool (extension) launches it.
See the Chimera Tools index
for descriptions of the individual tools.
If certain tools or extensions have been started and not quit during
a Chimera session, their instances
will appear in the bottom section of the Tools menu:
- Tool_name (or Tool_name - data)
- Raise - open the tool interface (if closed) and
bring it to the front
- Hide - close the tool interface without exiting
- Quit - exit from this instance of the tool
Favorites
The Favorites menu contains the
Preferences
in addition to any subset of the
Tools menu (individually specified
using the Tools preferences).
The default contents are
- Model Panel - open the
Model Panel, which lists the current models
and enables many operations upon them
- Side View - open the
Side View for easy adjustment of scale and clipping planes
- Command Line - show the
Command Line
- Reply Log - open the Reply Log
containing informational, warning, and error messages from Chimera
Help
Documentation pages requested from the Help menu
will be shown in a browser window.
- Search Documentation... bring up a dialog for
searching the local (bundled) Chimera documentation
(which includes the User's Guide,
Programmer's
Guide, and other items listed in the
Chimera documentation index)
One or more terms can be entered in the search field.
Combinations of terms can be indicated with
and, or, not and parentheses.
Separating terms with a space is equivalent to using and.
Pressing return (Enter) or clicking Search initiates the search.
Hits will be listed in the Search Results column as links to
the corresponding documentation.
- User's Guide - open the
Chimera User's Guide
- Tutorials - open the
Tutorials section of the Chimera User's Guide
- Context Help - describe the feature that is clicked next
(avoid clicking the top bar of a dialog, since
that will fail to bring up a help page)
- Check for Updates - report whether the version of Chimera being used
is older than the latest version available on the Web
(requires internet connectivity)
- Contact Us - show e-mail
addresses for asking questions or making suggestions
- Report a Bug... open a
form for bug submission
- Citation Info - show how
to cite usage of Chimera
- Registration... open a form for registration as a Chimera user
- About UCSF Chimera - report what version of Chimera is being used
and show copyright information
(like the command version)
UCSF Computer Graphics Laboratory / May 2008