Chimera Menus
The major menu headings are:
The menus are tear-off, as indicated by a dashed line
above the entries when the menu contents are shown.
Choosing the dashed line instead of an entry makes the menu
an independent window that remains up until explicitly closed.
Unavailable options are grayed out.
-
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
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)
- coil - amino acid residues not in helices or strands
- helix - amino acid residues in helices
- strand - amino acid residues in strands
- 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
-
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. If both the within and beyond options are checked,
only the atoms that fit both criteria will be selected, for example,
those within 12 Å but farther away than 8 Å.
- 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
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
- stick
(stick representation)
- ball & stick
(ball-and-stick representation)
- sphere
(sphere or CPK representation)
- wire
(wire representation)
- wire width
(see also the command linewidth)
- always affects entire molecule models even
though the targets may be narrower
- rings
(see also the commands fillring
and aromatic)
- aromatic rings can only be shown as filled when their aromaticity
display is turned off, and the aromaticity settings always affect entire
models even though the targets may be narrower
- fill thick
- fill thin
- fill off
- aromatic disk
- aromatic circle
- aromatic off
- nucleotide objects
(see also the command nucleotides)
- off - show atoms instead of sugar/base abstractions, remove any
nucleotide ring fill
- settings... open the
Nucleotides tool for controlling special nucleotide representations
- 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.
Even though the targets may be narrower,
representations (solid, mesh, and dot) always apply
to entire surface pieces
and transparency layer options always apply to entire
surface models.
- 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)
- one layer
- show only the topmost layer of a transparent surface
- all layers - show all layers of a transparent surface
- Color
(see also the command color)
- [top 20 colors]
- by heteroatom
- use a built-in
color-by-element scheme, except leaving carbon atoms unchanged
- by element
- use a built-in
color-by-element scheme
- 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 options...
open the Color Actions dialog
for access to all 60 colors
and finer control over which types of items are colored
(for example, background only or ribbons only)
- 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
(etc.)
Newly generated numerical, boolean, or string-valued atom
attributes will also be listed.
- residue
(see the command rlabel for
details, including label positioning)
- 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
and set the center of rotation method to
center of view (analogous to the command
focus);
if nothing is selected, set the
center of rotation method
to front center
- Set Pivot
- set the center of rotation to the center of the bounding sphere of the
targets
and set the center of rotation method to
fixed (analogous to the command
cofr);
if nothing is selected, set the
center of rotation method
to front center
- 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 naming style controls
the format of the specifications.
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
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 background color is set to black.
- The ribbons preset
shows most peptide and nucleic acid chains as ribbons,
plus atomic detail (excluding hydrogens on carbon atoms)
for residues within 3.5 Å
of a ligand residue or metal ion.
Atomic detail is also used for chains that are very short. Nucleic acids
may be shown with special sugar and base representations (as produced by
Nucleotides),
with the level of abstraction dependent on size.
- The all atoms preset
displays all atoms and bonds as wires with heteroatom
color-coding. Carbons are shown in the model colors so that models will be
distinguishable from one another.
- The hydrophobicity surface preset 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
(different color-codings can be applied with
rangecolor or
Render
by Attribute).
Surfaces of nonpeptides 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 background color is set to white.
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.
The Volume menu is a replica of the Tools... Volume Data menu.
It can be shown/hidden using
Tools... Volume Data... Volume Menu on Menubar
or the similar entry in the
Tools menu of
Volume Viewer.
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
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
Start-of-line aliases defined with the command
alias will be listed here.
Choosing an entry from the Aliases menu executes the alias.
The Aliases menu will only be present when there is
at least one start-of-line alias.
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
- Commands Index - open the Chimera
Commands Index
- 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 (requires internet connectivity)
- see if any production releases are newer than the
version in use, and if so, provide links to download them
- 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 / September 2010