Chimera Menus
The major menu headings are
File,
Select,
Actions,
Tools,
Favorites,
and Help.
Unavailable menu options are shown in a lighter color.
The menus are "tear-off," as indicated by dashed lines; choosing
the dashed line instead of a menu entry makes the menu
an independent widget that remains up until explicitly closed.
File
-
Open Session... bring up a dialog for
opening a previously saved
session (Python file)
- Save Session - save the current
session as session.py in the working directory
(uses
SimpleSession)
- Save Session As...
bring up a dialog for
saving
the current
session to a specified name and directory location
(uses
SimpleSession)
- Close Session - clear session contents without exiting from Chimera
- Save Image... open the Image Panel
for saving a TIFF file
Select
- Chain
(only chain IDs found in currently open structures will be listed)
- Chemistry
- Residue
- amino acid category
(note that the existing amino acid categories can be changed and new
categories defined and listed here, using
ResProp)
- name
(only residue names found in currently open structures will be listed)
- 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
- secondary structure (only applies to peptides/proteins)
- helix - residues in helices as defined by PDB HELIX records
in the input file, or if these are not present, using
ksdssp
- sheet - residues in strands as defined by PDB SHEET records
in the input file, or if these are not present, using
ksdssp
- turn - residues in turns as defined by PDB TURN records
in 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
(note that other categorizations can be defined and listed
in the top section of the Select menu,
using the Selector Construction
Panel; see Construct Selector...
below)
- Sequence... select by amino acid or nucleotide sequence
- Atom Specifier... use
atom specification syntax for selection
- 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
- 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
- Undo - undo the most recent selection operation
Actions
Actions are applied to items that have been
selected.
When nothing is selected,
the various operations
(Color,
Label,
Focus,
Atoms/Bonds,
Ribbon, and
Surface)
act on everything at the level specified by the
Target setting.
These operations act only on molecules and molecular surfaces;
other types of models will not be affected.
- Color
- Label
- off - undisplay atom labels
- name - label atoms by name
- element - label atoms by element
- IDATM type - label atoms by
atom type
- other...
label atoms with an arbitrary string or with
other atom-associated information:
- altLoc - alternate location identifier, if any,
from the input file
- bfactor - B-factor value, if any, from the input file
- defaultRadius -
default VDW radius
- occupancy - occupancy value, if any, from the input file
- 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)
- residue -
Residue labels are actually extra atom labels; the labeled
atom is CA in amino acid residues, C4' in nucleic acid residues,
and in other residue types, the atom with the name that falls first
in alphabetical order.
- off - undisplay residue labels
- name - label residues by name
- number - label residues by sequence number (including the
chain ID, if any)
- both - label residues by name and sequence number
- Focus
- focus the view on atoms, bonds, and/or ribbon segments
that are displayed. If any items are selected,
only those both selected and displayed are considered. Focusing consists of
- translating to center the item(s), scaling them to fill the view,
and moving the clipping planes to bracket the item(s) in the Z dimension
(like the command window)
- making the center of the bounding box of the item(s)
the center of rotation
(like the command cofr)
- Atoms/Bonds
- show
- hide
- backbone only
- only applied to residues in bonded chains containing amino acid
or nucleic acid moieties; includes 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
- only applied to residues in bonded chains containing amino acid
or nucleic acid moieties.
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'.
Choosing this turns
auto-chaining off.
- chain trace only
- only applied to residues in bonded chains containing amino acid
or nucleic acid moieties; includes one atom per residue, CA in each
amino acid and C4' in each nucleic acid residue.
Choosing this turns
auto-chaining on.
- wire width
- always affects entire molecule models even
though the selection may be narrower
- wire
(wireframe representation)
- stick
(stick representation)
- ball & stick
(ball-and-stick representation)
- sphere
(sphere or CPK representation)
- Ribbon
- secondary structure ribbon
(see also the commands ribbon
and ribrepr).
Ribbons are only drawn for proteins and nucleic acids.
Protein secondary structure is determined from HELIX and SHEET records
in the input file, or if these are not present, using
ksdssp.
- show
- hide
- flat
- edged
- round
- Surface
- molecular surface
(see also the commands surface
and surfrepr)
- Target (current_target)
- control whether actions
should apply only to selected atoms/bonds or to the entire residues,
chains, or models containing them (or the complement of any of these);
possible values of current_target are:
- selected atoms/bonds
- selected residues
- selected chains
- selected models
- unselected atoms/bonds
- unselected residues
- unselected chains
- unselected models
- realm (current_realm)
- only applies when the
Target is unselected atoms/bonds, unselected residues,
or unselected chains;
possible values of current_realm are:
- selected models - only act on unselected parts of models
containing selections
- all models - act on unselected parts of models containing
selections
and on models not containing any selections
- Inspect -
open the Selection Inspector,
which lists what items are selected, shows their properties, and allows
their properties to be changed
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 Tools section
of the
Chimera User's Guide 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
Selection of Help menu items opens a browser window containing the
requested information.
- Version Info - show what version of Chimera is being used
- Software Updates - report whether the version of Chimera being used
is older than the latest version available on the web
(requires internet connectivity)
- Feedback - show e-mail addresses for
reporting Chimera problems or making suggestions
- Citing Chimera - show how to cite usage of Chimera
- Registration... open the form for registration as a Chimera user