Command line interface
Sirius features a command line interface
that can be used in parallel with the menu-driven operations. Its primary
purpose is to speed up the most common visualization tasks and enable
saving sequences of commands to produce desired scenes that are compatible
with other applications (such as RasMol).
The command syntax is based on the set of
keywords used by RasMol, with the additional commands that are used to
operate multiple loaded structures, directly specify desired rendering
style and quality, as well as add atoms to an existing selection instead
of replacing it.
Important note: unlike RasMol,
SIrius uses coordinate axis direction and rotation conventions normally
accepted in computer graphics and molecular visualization software. For
instance, Y axis in Sirius is pointing upwards, while in RasMol it's directed
down. Additional differences concern direction of rotation. Therefore,
commands for translation along the Y axis, as well as rotation around
the Y axis will produce in Sirius the opposite result. However, for backward
compatibility, any imported RasMol scripts are automatically converted
to the Sirius coordinate system, so that you will still get the same view
as in RasMol. A checkbox in the Script menu indicates whether
the loaded script is treated as RasMol script or not. If you start editing
it and replace original commands with those specific to Sirius, be sure
to uncheck the box.
Full list of Sirius commands is given in
the table below. For additional description of RasMol commands please
refer to the RasMol manual, since it may help in becoming aquainted with
the commands used by Sirius. Also, this command line interface and script
interpreter are under development, and additional commands are likely
to be introduced. Any changes, however, should not affect syntax of the
existing commands, which will keep any scripts compatible with the future
versions of Sirius.
Command panel is activated
from the Tools menu. Note that the command panel is not a separate
window, and hence cannot be directly minimized. However, if it is
closed or the mark in the menu is unchecked, it becomes hidden rather
than deleted. Therefore, this approach can be used to temporarily
hide the panel - its contents will not be lost.
The panel has two parts: the large
text area and the command line field under it. The command line
is used to type individual commands in interactive mode. The command
is run when the Execute button is clicked or Enter key is pressed.
Once the command has run, it is copied to the text area to form
history of executed commands. In addition, the entire list of commands
in the text area can be executed by selecting Script->Run menu
The text area can also be used to paste
existing scripts or display imported scripts.
Sirius command reference
|| Adds specified
atom set to the existing selection
|| If more
than one structure is loaded, it is necessary to specify which structure
the commands should apply to. To do so, enter attach <structure
name>. Names of loaded structures appear in any appearance
dialog's pulldown menu or under File->Close structure
|| This command
followed by color name or comma separated RGB values sets the color
of the 3D workspace background.
cartoon ribbon in the current selection. Cartoon ribbon contains flat
strands with arrowheads and wide helices.
the command panel's text area and command line.
any loaded structures.
color of the currently selected atoms. Can be followed by color
name (red, blue, etc.), name of the color set (amino, cpk, structure,
etc.) or comma-separated RGB triplet enclosed in square brackets.
For specific information about predefined color schemes, refer to
the RasMol manual.
Sample command: color [100,100,230]
a named set of atoms. The command needs to be followed by name for
the new set and the list of atoms or residues that should be in the
set. For more complex set definitions (e.g., based on distance), it's
recommended to use the interactive approach: Structure->Define/edit
a dot surface around selected atoms. Dot density is defined by the
number that follows the keyword. Value of less than 200 produces a
medium quality surface, values between 200 adn 600 generate a high
quality surface, while higher numbers result in an ultra quality surface
(for comparison, refer to the Surface dialog).
|| Loads a
structure from a file. Command is followed by file name. If full path
is not given, it is assumed that the file is located in the current
working directory (refer to Preferences). File type is determined
from the extension.
|| Same as
translate - used to move the structure in the direction of coordinate
axes. Is added to simplify typing and reduce spelling errors
rendering state of atoms and bonds in the selection. Is followed by
keywords that specify the style and (optional) quality. These are:
lines, stick, ballstick and spacefill.
Quality can be indicated by adding best keyword after the
style specification. If no quality is requested, the structure is
rendered as fast.
the view to its original location and orientation. Rendering and other
appearance is not changed. If a total reset is needed, the structure
can simply be reloaded.
a visible ribbon for selected atoms. In the case of ribbon off,
the ribbon is hidden.
the structure around the specified axis followed by angle in degrees.
Direction of rotation is defined by the sign of the angle value. For
example, rotate x 45 will rotate the structure around x axis
by 45 degrees, with the closest point moving up. Positive value for
the y axis indicates that the closest point will move left, and for
z axis positive value results in clockwise rotation.
command causes a set of atoms to be selected for further operations.
A set of atoms can be given in a variety of different methods.
- named set
(ligand, protein, basic, etc.)
names (ala, gly, tyr, etc.)
- nucleic acid
names (g, c, etc.)
- element names
(N, Ca, Mg)
- residue numbers
- residue names
with numbers (ala230)
- residue names
with numbers and chain ids (ala230E)
- atom names
- fully qualified
atom names (ala230e.ca)
These sets can
be combined using comma-separated lists (2,4,5,6,9), dash-separated
ranges of residue numbers (100-320), wild cards (*E indicates all
atoms in chain E), parentheses and logical operators (and, or, not).
between two sets returns a union of the sets - only atoms present
in both sets form the resulting set. E.g. select ala230 and
sidechain highlights only side chain atoms in the alanine 230.
adds the two sets. For example, select ala or tyr will
select all alanine and tyrosine residues int he structure.
will exclude atoms of the second set from the atoms of the first
set. For example, select ala230 and not ca will highlight
the entire residue except for the CA.
A full list of predefined named sets
is given below.
Command addselect follows exactly the
same syntax rules, except it doesn't clear the previous selection.
|| Used in
combination with strands and a numeric value, sets the following
strands representation to a thin backbone trace. E.g., set strands
selected atoms using spacefilling representation.
a ribbon for the selected atoms. If a set strands 1 was entered
before, a thin backbone trace is created.
a uniform ribbon for selected residues. The ribbon has round cross-section.
|| Moves the
structure in the direction of one of the three coordinate axes. For
example, translate x 10 will move the structure by 10 angstroms to
the right. Positive directions for the axes: x - right, y - up, z
- closer to the point of view.
|| This command
indicates whether the atomic structure should be displayed. For example,
wireframe off causes the atoms and bonds to become hidden.
Just the wireframe command with no additional parameters
causes the structure to appear. This command doesn't affect displayed
|| Same as
close, and used for compatibility with existing RasMol scripts.
Predefined named sets
All acidic amino acids
All acyclic amino acids
|| All aliphatic
|| All alpha
|| All aminoacids
|| All aromatic
atoms in protein or DNA structures
|| All basic
that are bonded to at least one other atom
acids with propensity to be buried (not their actual location in the
|| All charged
amino acids (both aromatic and non-aromatic)
All amino acids that are in a helix (their actual
atoms in the protein/DNA structure (denoted as HETATM in PDB files)
|| All hydrogen
|| All hydrophobic
acids with large side chains
that are not amino acids, nucleic acids or solvent
acids with medium-sized side chains
|| All nucleic
|| All polar
|| All amino
|| All amino
acids in beta-strands
|| Side chains
of all amino acids
|| All amino
acids with small side chains
|| Amino acids
with propensity to form protein surface (not their actual location)
|| All amino
acids in secondary structure turns
|| All water
Predefined color schemes
used for amino acid coloring in RasMol
Colors residues according to the secondary structure element they
are located in. Specific colors that correspond to helices, strands,
etc. can be set in Structure Viewer tab of the Preferences
CPK coloring scheme used in RasMol