RASMOL(1) | General Commands Manual | RASMOL(1) |
NAME¶
rasmol - Molecular Graphics Visualisation Tool v2.7.5SYNOPSIS¶
rasmol [-nodiplay] [[-format ] filename] [-script scriptfile]FORMATS¶
- -pdb
- Protein Data Bank
- -mdl
- MDL's MOL File Format
- -mol2
- Tripos' Sybyl MOL2 Format
- -xyz
- MSC's XYZ (XMol) Format
- -mopac
- MOPAC Input or Output File Format
- -alchemy
- Alchemy File Format
- -charmm
- CHARMm File Format
- -cif
- IUCr CIF or CIF File Format
NOTICES¶
This software has been created from several sources. Much of the code is from RasMol 2.6, as created by Roger Sayle. The torsion angle code, new POVRAY3 code and other features are derived from the RasMol2.6x1 revisions by Arne Mueller. The Ramachandran printer plot code was derived from fisipl created by Frances C. Bernstein. See the Protein Data Bank program tape.and help CIFPARSE for applicable notices. Please type help copyright for copyright notices. If you use RasMol V2.6 or an earlier version, type the RasMol command help oldnotice.
COPYING¶
This version is based directly on RasMol version 2.7.4.2, on RasMol verion 2.7.4.2, on RasMol version 2.7.4, on RasMol version 2.7.3.1, on RasMol version 2.7.3, on RasMol version 2.7.2.1.1, Rasmol version 2.7.2, RasMol version 2.7.1.1 and RasTop version 1.3 and indirectly on the RasMol 2.5-ucb and 2.6-ucb versions and version 2.6_CIF.2, RasMol 2.6x1 and RasMol_2.6.4.http://www.gnu.org/licenses/gpl.txt
- GPL
-
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.
59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Library General Public License instead.) You can apply it to your programs, too.
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We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software.
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GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you".
1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.
2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
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b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
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c) If the modified program normally reads commands interactively
when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
announcement including an appropriate copyright notice and a
notice that there is no warranty (or else, saying that you provide
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the Program is not required to print an announcement.)
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How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.
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Gnomovision version 69, Copyright (C) year name of author
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- RASLIC
- If you do not use the GPL, the following license terms
apply:
1. Either include the complete documentation, especially the file NOTICE, with what you distribute or provide a clear indication where people can get a copy of the documentation; and
2. Please give credit where credit is due citing the version and original authors properly; and
3. Please do not give anyone the impression that the original authors are providing a warranty of any kind.
4. Please explain in your documentation how what you did differs from this version of RasMol; and
5. Please make your modified source code available.
- General Notice
- The following notice applies to this work as a whole and to
the works included within it:
- RasMol V2.6 Notice
- The following notice applies to RasMol V 2.6 and older
RasMol versions.
- IUCR Policy
- The IUCr Policy for the Protection and the Promotion of
the STAR File and CIF Standards for Exchanging and Archiving
Electronic Data.
* holds the copyrights on the standards themselves,
* owns the associated trademarks and service marks, and
* holds a patent on the STAR File.
* Software claiming to read files written to either the STAR File or the CIF standard must be able to extract the pertinent data from a file conformant to the STAR File syntax, or the CIF syntax, respectively.
* Software claiming to write files in either the STAR File, or the CIF, standard must produce files that are conformant to the STAR File syntax, or the CIF syntax, respectively.
* Software claiming to read definitions from a specific data dictionary approved by the IUCr must be able to extract any pertinent definition which is conformant to the dictionary definition language (DDL)[3] associated with that dictionary.
- CBFLIB
- The following Disclaimer Notice applies to CBFlib V0.1,
from which this code in part is derived.
- CIFPARSE
- Portions of this software are loosely based on the CIFPARSE
software package from the NDB at Rutgers University. See
http://ndbserver.rutgers.edu/NDB/mmcif/software
DESCRIPTION¶
RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server.the molecules may be rotated and translated.
COMMANDS¶
RasMol allows the execution of interactive commands typed at the RasMol> prompt in the terminal window. Each command must be given on a separate line. Keywords are case insensitive and may be entered in either upper or lower case letters. All whitespace characters are ignored except to separate keywords and their arguments.- Backbone
- The RasMol backbone command permits the
representation of a polypeptide backbone as a series of bonds connecting
the adjacent alpha carbons of each amino acid in a chain. The display of
these backbone 'bonds' is turned on and off by the command parameter in
the same way as with the wireframe command. The command backbone
off turns off the selected 'bonds', and backbone on or with a
number turns them on. The number can be used to specify the cylinder
radius of the representation in either Angstrom or RasMol units. A
parameter value of 500 (2.0 Angstroms) or above results in a
"Parameter value too large" error. Backbone objects may be
coloured using the RasMol colour backbone command.
- Background
- The RasMol background command is used to set the
colour of the "canvas" background. The colour may be given as
either a colour name or a comma separated triple of Red, Green and Blue
(RGB) components enclosed in square brackets. Typing the command help
colours will give a list of the predefined colour names recognised by
RasMol. When running under X Windows, RasMol also recognises colours in
the X server's colour name database.
- Bond
- The RasMol command bond <number> <number>
+ adds the designated bond to the drawing, increasing the bond order
if the bond already exists. The command bond <number>
<number> pick selects the two atoms specified by the atom serial
numbers as the two ends of a bond around which the rotate bond
<angle> command will be applied. If no bond exists, it is
created.
- Bulgarian
- The RasMol Bulgarian command sets the menus and
messages to the Bulgarian versions.
- Cartoon
- The RasMol cartoon command does a display of a
molecule ribbons as Richardson (MolScript) style protein
cartoons, implemented as thick (deep) ribbons. The easiest way to
obtain a cartoon representation of a protein is to use the Cartoons
option on the Display menu. The cartoon command represents
the currently selected residues as a deep ribbon with width specified by
the command's argument. Using the command without a parameter results in
the ribbon's width being taken from the protein's secondary structure, as
described in the ribbons command. By default, the C-termini of
beta-sheets are displayed as arrow heads. This may be enabled and disabled
using the set cartoons command. The depth of the cartoon may be
adjusted using the set cartoons <number> command. The set
cartoons command without any parameters returns these two options to
their default values.
- Centre
- The RasMol centre command defines the point about
which the rotate command and the scroll bars rotate the current
molecule. Without a parameter the centre command resets the centre of
rotation to be the centre of gravity of the molecule. If an atom
expression is specified, RasMol rotates the molecule about the centre of
gravity of the set of atoms specified by the expression. Hence, if a
single atom is specified by the expression, that atom will remain
'stationary' during rotations.
- Chinese
- The RasMol Chinese command sets the menus and
messages to the Chinese versions.
- Clipboard
- The RasMol clipboard command places a copy of the
currently displayed image on the local graphics 'clipboard'. Note: this
command is not yet supported on UNIX or VMS machines. It is intended to
make transferring images between applications easier under Microsoft
Windows or on an Apple Macintosh.
- Colour
- Colour the atoms (or other objects) of the selected region.
The colour may be given as either a colour name or a comma separated
triple of Red, Green and Blue (RGB) components enclosed in square
brackets. Typing the command help colours will give a list of all
the predefined colour names recognised by RasMol.
- ColourMode
- ColourMode allows the user to switch between using the new
colour method. At present, the new coloring technique is the same
as the old one, but to preserve compatibility for older scripts it may be
wise to add a "colormode on" near the top of your script
somewhere, if the script was designed for version 2.7.3 of RasMol or
earlier. The new color method, when completed, aims to fix a few bugs in
the coloring routines.
- Connect
- The RasMol connect command is used to force RasMol
to (re)calculate the connectivity of the current molecule. If the original
input file contained connectivity information, this is discarded. The
command connect false uses a fast heuristic algorithm that is
suitable for determining bonding in large bio-molecules such as proteins
and nucleic acids. The command connect true uses a slower more
accurate algorithm based upon covalent radii that is more suitable to
small molecules containing inorganic elements or strained rings. If no
parameters are given, RasMol determines which algorithm to use based on
the number of atoms in the input file. Greater than 255 atoms causes
RasMol to use the faster implementation. This is the method used to
determine bonding, if necessary, when a molecule is first read in using
the load command.
- Defer
- The RasMol defer command adds the command given to
the macro with given name, if no name is given, the command is added to
the macro with a blank name. The command zap is a special case. In
that case the macro is erased. If no name is given the command must begin
with a selection, e.g. defer (selection).spacefill
- Define
- The RasMol define command allows the user to
associate an arbitrary set of atoms with a unique identifier. This allows
the definition of user-defined sets. These sets are declared statically,
i.e. once defined the contents of the set do not change, even if the
expression defining them depends on the current transformation and
representation of the molecule.
- Depth
- The RasMol depth command enables, disables or
positions the back-clipping plane of the molecule. The program only draws
those portions of the molecule that are closer to the viewer than the
clipping plane. Integer values range from zero at the very back of the
molecule to 100 which is completely in front of the molecule. Intermediate
values determine the percentage of the molecule to be drawn.
- Dots
- The RasMol dots command is used to generate a van
der Waals' dot surface around the currently selected atoms. Dot surfaces
display regularly spaced points on a sphere of van der Waals' radius about
each selected atom. Dots that would are 'buried' within the van der Waals'
radius of any other atom (selected or not) are not displayed. The command
dots on deletes any existing dot surface and generates a dots
surface around the currently selected atom set with a default dot density
of 100. The command dots off deletes any existing dot surface. The
dot density may be specified by providing a numeric parameter between 1
and 1000. This value approximately corresponds to the number of dots on
the surface of a medium sized atom.
- Echo
- The RasMol echo command is used to display a message
in the RasMol command/terminal window. The string parameter may optionally
be delimited in double quote characters. If no parameter is specified, the
echo command displays a blank line. This command is particularly
useful for displaying text from within a RasMol script file.
- English
- The RasMol English command sets the menus and
messages to the English versions.
- Execute
- The RasMol execute command:
- French
- The RasMol French command sets the menus and
messages to the French versions.
- HBonds
- The RasMol hbond command is used to represent the
hydrogen bonding of the protein molecule's backbone. This information is
useful in assessing the protein's secondary structure. Hydrogen bonds are
represented as either dotted lines or cylinders between the donor and
acceptor residues. The first time the hbond command is used, the
program searches the structure of the molecule to find hydrogen bonded
residues and reports the number of bonds to the user. The command
hbonds on displays the selected 'bonds' as dotted lines, and the
hbonds off turns off their display. The colour of hbond objects may
be changed by the colour hbond command. Initially, each hydrogen
bond has the colours of its connected atoms.
- Help
- The RasMol help command provides on-line help on the
given topic.
- Italian
- The RasMol Italian command sets the menus and
messages to the Italian versions.
- Japanese
- The RasMol Japanese command sets the menus and
messages to the Japanese versions.
- Label
- The RasMol label command allows an arbitrary
formatted text string to be associated with each currently selected atom.
This string may contain embedded 'expansion specifiers' which display
properties of the atom being labelled. An expansion specifier consists of
a '%' character followed by a single alphabetic character specifying the
property to be displayed. An actual '%' character may be displayed by
using the expansion specifier '%%'.
using the set fontstroke
command.
- Load
- Load a molecule coordinate file into RasMol. Valid molecule
file formats are pdb (Protein Data Bank format), mdl
(Molecular Design Limited's MOL file format), alchemy (Tripos'
Alchemy file format), mol2 (Tripos' Sybyl Mol2 file format),
charmm (CHARMm file format), xyz (MSC's XMol XYZ file
format), mopac (J. P. Stewart's MOPAC file format) or cif
(IUCr CIF or mmCIF file format). If no file format is specified,
PDB, CIF, or mmCIF is assumed by default. Up to 20
molecules may be loaded at a time. If CHEM_COMP ligand models are included
in an mmCIF file, they will be loaded as NMR models, first giving the all
the NMR models for model coordinates if specified and then giving all the
NMR models for ideal model coordinates.
- Map
- The RasMol map commands manipulate electron density
maps in coordination with the display of molecules. These commands are
very memory intensive and may not work on machines with limited memory.
Each molecule may have as many maps as available memory permits. Maps may
be read from files or generated from Gaussian density distributions around
atoms.
- Map colour
- The RasMol map colour command colours the selected
maps according to the specified colour scheme. The colour scheme may be a
colour name or and RBG triple in brackets, or the keyword atom to
cause the map points to be coloured by the color of the nearest atom.
- Map generate
- The RasMol map generate command generates a map from
whatever atoms are currently selected, by summing electron densities
approximated by Gaussian distributions. The height of each Gaussian is
determined by the setting of the map scale command. In the default
of map scale true, each Gaussian has a height proportional element type of
the atom. If the optional 'LRSurf' parameter is given or if map scale
false has been executed, each Gaussian is scaled so that the Gaussian
contour level 1 is at the van der Waals radius. In either case a standard
deviation determined by the most recently specified spread or resolution
is used. If a non-zero spread has been given the radius of the atom is
multiplied by the spread to find the standard deviation. The default is
2/3rds. If a resolution has been given, the spread is inferred as 2/3rds
of the resolution.
- Map level
- The RasMol map level command sets the contour level
to be used in creating subsequent representations of generated or loaded
maps. If the keyword MEAN in used the level is relative to the mean of the
map data. Otherwise the level is absolute.
- Map load
- The RasMol map load command loads a map file into
RasMol. The valid formats are CCP4 map format and imgCIF format.
- Map mask
- The RasMol map mask command specifies a mask to be
used to limit the display space to be used for making representations of
other maps or removes an earlier mask specification.
- Map resolution
- The RasMol map resolution command specifies the
resolution in RasMol units or, if a number containing a decimal point is
given, the resolution in Angstroms to be used in generating and in
representing maps.
- Map restrict
- The RasMol map restrict command selects particular
maps to make them active for subsequent map commands. This is similar to
the map select command, but does disables the display of the maps
that were not selected.
- Map save
- The RasMol map save command saves an imgCIF map
file.
- Map scale
- The RasMol map scale command selects the scaling of
pseudo-Gaussians in the map generate commands. In the default of
map scale true, each Gaussian has a height proportional element type of
the atom. If map scale false has been executed, each Gaussian is scaled so
that the Gaussian contour level 1 is at the van der Waals radius. In
either case a standard deviation determined by the most recently specified
spread or resolution is used.
- Map select
- The RasMol map select command selects particular
maps to make them active for subsequent map commands. This is similar to
the map restrict command, but does not disable the display of the
maps that were not selected.
- Map show
- The RasMol map show command causes information about
the maps specified by the map selector to be written to the command
window.
- Map spacing
- The RasMol map spacing command specifies the spacing
to be used between contour lines in creating representations of maps. The
spacing is typically
given in Angstroms with a decimal point, but may also be specified in RasMol units (250ths of an Angstom) as an integer. For maps loaded in grid coordinates that spacing is parallel to the cell edges. The default spacing is one half Angstrom.
- Map spread
- The RasMol map spread command specifies the
reciprocal of the number of standard deviations per radius to be used in
generating maps as sums of Gaussians centered on atomic positions. The
default spread is one two thirds (i.e. each radius covers 1.5 standard
deviations).
- Map zap
- The RasMol map zap command removes the data and
representations of the maps specified by the map selector. The map numbers
of maps that have not been removed are not changed.
- Molecule
- The RasMol molecule command selects one of up to 5
previously loaded molecules for active manipulation. While all the
molcules are displayed and may be rotated collectively (see the rotate
all command), only one molecule at a time time is active for
manipulation by the commands which control the details of rendering.
- Monitor
- The RasMol monitor command allows the display of
distance monitors. A distance monitor is a dashed (dotted) line between an
arbitrary pair of atoms, optionally labelled by the distance between them.
The RasMol command monitor <number> <number> adds such
a distance monitor between the two atoms specified by the atom serial
numbers given as parameters
- Notoggle
- The RasMol NoToggle command enables or disables the
use of the toggle ability that is used by some of the other RasMol
commands. When no boolean value is specified, NoToggle mode is ENABLED.
When NoToggle mode is ENABLED, all toggle functionality is DISABLED. To
turn it off, one must explicitly set notoggle off.
- Pause
- The RasMol pause command is used in script files to
stop the script file for local manipulation by a mouse, until any key is
pushed to restart the script file. Wait is synonymous with
pause. This command may be executed in RasMol script files to
suspend the sequential execution of commands and allow the user to examine
the current image. When RasMol executes a pause command in a script
file, it suspends execution of the rest of the file, refreshes the image
on the screen and allows the manipulation of the image using the mouse and
scroll bars, or resizing of the graphics window. Once a key is pressed,
control returns to the script file at the line following the pause
command. While a script is suspended the molecule may be rotated,
translated, scaled, slabbed and picked as usual, but all menu commands are
disabled.
- Play
- The RasMol play command specifies the recording
medium from which to play back a movie. The playback frame start time is
given in seconds to millisecond precision. Since we are working on
computers, the medium is specified as a set of files, each marked with the
playback frame start time in milliseconds as part of the name. The place
in the name at which to look for the playback frame start time in
milliseconds is marked by the characters "ssssss" with an
appropriate number of digits. RasMol accepts either upper or lower case
s's or decimal digits to mark the place for the time. The play off and
play eject commands effectively remove the specified medium from use. If
no medium is specified, play off suspends playing and play on resumes
playing. Normally play starts immediately and runs to the end of the
medium. However, if play off and/or or some combination of play from and
play until is entered before play type medium, those settings will
be used.
- The RasMol print command sends the currently
displayed image to the local default printer using the operating system's
native printer driver. Note: this command is not yet supported under UNIX
or VMS. It is intended to take advantage of Microsoft Windows and Apple
Macintosh printer drivers. For example, this allows images to be printed
directly on a dot matrix printer.
- Quit
- Exit from the RasMol program. The RasMol commands
exit and quit are synonymous, except within nested scripts.
In that case, exit terminates only the current level, while
quit terminates all nested levels of scripts.
- Record
- The RasMol record command specifies the recording
medium to hold the movie. Since we are working on computers, the medium is
specified as a template for a set of files, each marked with the playback
frame start time in milliseconds (rather than as seconds to avoid
embedding a decimal point) as part of the name. The place in the name to
be replaced with the playback frame start time in milliseconds is marked
by the characters "ssssss" with an appropriate number of digits.
RasMol accepts either upper or lower case s's or decimal digits to mark
the place for the time. The record off commands remove the specified
medium from use. If no medium is specified, record off suspends recording
and record on resumes recording with the next available time on the same
medium. The screen is the default medium and is, by default, on. Writing
to disk must be explicitly specified so that the disk does not get filled
up unintentionally. The type of a recording medium may be an image type
such as gif, pict or png to record the actual screen images or script to
record the RasMol commands used to generate the frames.
- Refresh
- The RasMol refresh command redraws the current
image. This is useful in scripts to ensure application of a complex list
of parameter changes.
- Renumber
- The RasMol renumber command sequentially numbers the
residues in a macromolecular chain. The optional parameter specifies the
value of the first residue in the sequence. By default, this value is one.
For proteins, each amino acid is numbered consecutively from the N
terminus to the C terminus. For nucleic acids, each base is numbered from
the 5' terminus to the 3' terminus. All chains in the current database are
renumbered and gaps in the original sequence are ignored. The starting
value for numbering may be negative.
- Reset
- The RasMol reset command restores the original
viewing transformation and centre of rotation. The scale is set to its
default value, zoom 100, the centre of rotation is set to the
geometric centre of the currently loaded molecule, centre all, this
centre is translated to the middle of the screen and the viewpoint set to
the default orientation.
- Restrict
- The RasMol restrict command both defines the
currently selected region of the molecule and disables the representation
of (most of) those parts of the molecule no longer selected. All
subsequent RasMol commands that modify a molecule's colour or
representation affect only the currently selected region. The parameter of
a restrict command is a RasMol atom expression that is evaluated
for every atom of the current molecule. This command is very similar to
the RasMol select command, except restrict disables the
wireframe, spacefill and backbone representations in
the non-selected region.
- Ribbons
- The RasMol ribbons command displays the currently
loaded protein or nucleic acid as a smooth solid "ribbon"
surface passing along the backbone of the protein. The ribbon is drawn
between each amino acid whose alpha carbon is currently selected. The
colour of the ribbon is changed by the RasMol colour ribbon
command. If the current ribbon colour is none (the default), the
colour is taken from the alpha carbon at each position along its length.
- Rotate
- Rotate the molecule about the specified axis. Permitted
values for the axis parameter are "x", "y",
"z" and "bond". The integer parameter states the angle
in degrees for the structure to be rotated. For the X and Y axes, positive
values move the closest point up and right, and negative values move it
down and left, respectively. For the Z axis, a positive rotation acts
clockwise and a negative angle anti-clockwise.
- Russian
- The RasMol Russian command sets the menus and
messages to the Russian versions.
- Save
- Save the currently selected set of atoms in a Protein Data
Bank (PDB), MDL, Alchemy(tm) or XYZ format file. The distinction between
this command and the RasMol write command has been dropped. The
only difference is that without a format specifier the save command
generates a PDB file and the write command generates a
GIF image.
- Script
- The RasMol script command reads a set of RasMol
commands sequentially from a text file and executes them. This allows
sequences of commonly used commands to be stored and performed by single
command. A RasMol script file may contain a further script command up to a
maximum "depth" of 10, allowing complicated sequences of actions
to be executed. RasMol ignores all characters after the first '#'
character on each line allowing the scripts to be annotated. Script files
are often also annotated using the RasMol echo command.
- Select
- Define the currently selected region of the molecule. All
subsequent RasMol commands that manipulate a molecule or modify its colour
or representation only affect the currently selected region. The parameter
of a select command is a RasMol expression that is evaluated for
every atom of the current molecule. The currently selected (active) region
of the molecule are those atoms that cause the expression to evaluate
true. To select the whole molecule use the RasMol command select
all. The behaviour of the select command without any parameters
is determined by the RasMol hetero and hydrogen parameters.
- Set
- The RasMol set command allows the user to alter
various internal program parameters such as those controlling rendering
options. Each parameter has its own set or permissible parameter options.
Typically, omitting the parameter option resets that parameter to its
default value. A list of valid parameter names is given below.
- Show
- The RasMol show command display details of the
status of the currently loaded molecule. The command show
information lists the molecule's name, classification, PDB code and
the number of atoms, chains, groups it contains. If hydrogen bonding,
disulphide bridges or secondary structure have been determined, the number
of hbonds, ssbonds, helices, ladders and turns are also displayed,
respectively. The command show centre shows any non-zero centering
values selected by the centre [CenX, CenY, CenZ] command. The
command show phipsi shows the phi and psi angles of the currently
selected residues and the omega angles of cis peptide bonds. The command
show RamPrint (or 'show RPP' or 'show RamachandranPrinterPlot')
shows a simple Ramachandran printer plot in the style of Frances
Bernstein's fisipl program. The command show rotation (or 'show
rot' or 'show 'rotate') shows the currently selected values of z, y, x and
bond rotations, if any. The command show selected (or 'show
selected group' or 'show selected chain' or 'show selected atom' ) shows
the groups (default), chains or atoms of the current selection. The
command show sequence lists the residues that comprise each chain
of the molecule. The command show symmetry shows the space group
and unit cell of the molecule. The command show translation shows
any non-zero translation values selected by the translate <axis>
<value> command. The command show zoom shows any non-zero
zoom value selected by the zoom <value> command.
- Slab
- The RasMol slab command enables, disables or
positions the z-clipping plane of the molecule. The program only draws
those portions of the molecule that are further from the viewer than the
slabbing plane. Integer values range from zero at the very back of the
molecule to 100 which is completely in front of the molecule. Intermediate
values determine the percentage of the molecule to be drawn.
- Spacefill
- The RasMol spacefill command is used to represent
all of the currently selected atoms as solid spheres. This command is used
to produce both union-of-spheres and ball-and-stick models of a molecule.
The command, spacefill true, the default, represents each atom as a
sphere of van der Waals radius. The command spacefill off turns off
the representation of the selected atom as spheres. A sphere radius may be
specified as an integer in RasMol units (1/250th Angstrom) or a value
containing a decimal point. A value of 500 (2.0 Angstroms) or greater
results in a "Parameter value too large" error.
- Spanish
- The RasMol Spanish command sets the menus and
messages to the Spanish versions.
- SSBonds
- The RasMol ssbonds command is used to represent the
disulphide bridges of the protein molecule as either dotted lines or
cylinders between the connected cysteines. The first time that the
ssbonds command is used, the program searches the structure of the
protein to find half-cysteine pairs (cysteines whose sulphurs are within 3
Angstroms of each other) and reports the number of bridges to the user.
The command ssbonds on displays the selected "bonds" as
dotted lines, and the command ssbonds off disables the display of
ssbonds in the currently selected area. Selection of disulphide bridges is
identical to normal bonds, and may be adjusted using the RasMol set
bondmode command. The colour of disulphide bonds may be changed using
the colour ssbonds command. By default, each disulphide bond has
the colours of its connected atoms.
- Star
- The RasMol star command is used to represent all of
the currently selected atoms as stars (six strokes, one each in the x, -x,
y, -y, z and -z directions). The commands select not bonded
followed by star 75 are useful to mark unbonded atoms in a
wireframe display with less overhead than provided by spacefill
75. This can be done automatically for all subsequent wireframe
displays with the command set bondmode not bonded.
- Stereo
- The RasMol stereo command provides side-by-side
stereo display of images. Stereo viewing of a molecule may be turned on
(and off) either by selecting Stereo from the Options menu,
or by typing the commands stereo on or stereo off.
command.) It is not supported in vector PostScript output files, is not saved by the write script command, and in general is not yet properly interfaced with several other features of the program.
- Strands
- The RasMol strands command displays the currently
loaded protein or nucleic acid as a smooth "ribbon" of
depth-cued curves passing along the backbone of the protein. The ribbon is
composed of a number of strands that run parallel to one another along the
peptide plane of each residue. The ribbon is drawn between each amino acid
whose alpha carbon is currently selected. The colour of the ribbon is
changed by the RasMol colour ribbon command. If the current ribbon
colour is none (the default), the colour is taken from the alpha
carbon at each position along its length. The central and outermost
strands may be coloured independently using the colour ribbon1 and
colour ribbon2 commands, respectively. The number of strands in the
ribbon may be altered using the RasMol set strands command.
- Structure
- The RasMol structure command calculates secondary
structure assignments for the currently loaded protein. If the original
PDB file contained structural assignment records (HELIX, SHEET and TURN)
these are discarded. Initially, the hydrogen bonds of the current molecule
are found, if this hasn't been done already. The secondary structure is
then determined using Kabsch and Sander's DSSP algorithm. Once finished
the program reports the number of helices, strands and turns found.
- Surface
- The RasMol surface command renders a Lee-Richards
molecular surface resulting from rolling a probe atom on the selected
atoms. The value given specifies the radius of the probe. If given in the
first form, the evolute of the surface of the probe is shown (the solvent
excluded surface). If given in the second form, the envelope of the
positions of the center of the probe is shown (the solvent accessible
surface).
- Trace
- The RasMol trace command displays a smooth spline
between consecutive alpha carbon positions. This spline does not pass
exactly through the alpha carbon position of each residue, but follows the
same path as ribbons, strands and cartoons. Note that
residues may be displayed as ribbons, strands,
cartoons or as a trace. Enabling one of these
representations disables the others. However, a residue may be displayed
simultaneously as backbone and as one of the above representations. This
may change in future versions of RasMol. Prior to version 2.6,
trace was synonymous with backbone.
- Translate
- The RasMol translate command moves the position of
the centre of the molecule on the screen. The axis parameter specifies
along which axis the molecule is to be moved and the integer parameter
specifies the absolute position of the molecule centre from the middle of
the screen. Permitted values for the axis parameter are "x",
"y" and "z". Displacement values must be between -100
and 100 which correspond to moving the current molecule just off the
screen. A positive "x" displacement moves the molecule to the
right, and a positive "y" displacement moves the molecule down
the screen. The pair of commands translate x 0 and translate y
0 centres the molecule on the screen.
- UnBond
- The RasMol command unbond <number>
<number> removes the designated bond from the drawing.
- Wireframe
- The RasMol wireframe command represents each bond
within the selected region of the molecule as a cylinder, a line or a
depth-cued vector. The display of bonds as depth-cued vectors (drawn
darker the further away from the viewer) is turned on by the command
wireframe or wireframe on. The selected bonds are displayed
as cylinders by specifying a radius either as an integer in RasMol units
or containing a decimal point as a value in Angstroms. A parameter value
of 500 (2.0 Angstroms) or above results in an "Parameter value too
large" error. Bonds may be coloured using the colour bonds
command.
- Write
- Write the current image to a file in a standard format.
Currently supported image file formats include bmp (Microsoft
bitmap) and gif (Compuserve GIF), iris (IRIS RGB),
ppm (Portable Pixmap), ras (Sun rasterfile), ps and
epsf (Encapsulated PostScript), monops (Monochrome
Encapsulated PostScript), pict (Apple PICT), vectps (Vector
Postscript). The write command may also be used to generate command
scripts for other graphics programs. The format script writes out a
file containing the RasMol script commands to reproduce the current
image. The format molscript writes out the commands required to
render the current view of the molecule as ribbons in Per Kraulis'
Molscript program and the format kinemage the commands for David
Richardson's program Mage. The following formats are useful for further
processing: povray (POVRay 2), povray3 (POVRay 3 -- under
development), vrml (VRML file). Finally, several formats are
provided to provide phi-psi data for listing or for phipsi (phi-psi
data as an annotated list with cis omegas), ramachan and RDF
and RamachandranDataFile (phi-psi data as columns of numbers for
gnuplot), RPP and RamachandranPrinterPlot (phi-psi data as a
printer plot).
- Zap
- Deletes the contents of the current database and resets
parameter variables to their initial default state.
- Zoom
- Change the magnification of the currently displayed image.
Boolean parameters either magnify or reset the scale of current molecule.
An integer parameter specifies the desired magnification as a percentage
of the default scale. The minimum parameter value is 10; the maximum
parameter value is dependent upon the size of the molecule being
displayed. For medium sized proteins this is about 500.
SET PARAMETERS¶
RasMol has a number of internal parameters that may be modified using the set command. These parameters control a number of program options such as rendering options and mouse button mappings.picking play.fps radius record.aps
- Set Ambient
- The RasMol ambient parameter is used to control the
amount of ambient (or surrounding) light in the scene. The ambient
value must be between 0 and 100. It controls the percentage intensity of
the darkest shade of an object. For a solid object, this is the intensity
of surfaces facing away from the light source or in shadow. For depth-cued
objects this is the intensity of objects furthest from the viewer.
- Set Axes
- The RasMol axes parameter controls the display of
orthogonal coordinate axes on the current display. The coordinate axes are
those used in the molecule data file, and the origin is the centre of the
molecule's bounding box. The set axes command is similar to the
commands set boundbox and set unitcell that display the
bounding box and the crystallographic unit cell, respectively.
- Set Backfade
- The RasMol backfade parameter is used to control
backfade to the specified background colour, rather than black. This is
controlled by the commands set backfade on and set backfade
off. For example, this may be used to generate depth-cued images that
fade to white, rather than black.
- Set Background
- The RasMol background parameter is used to set the
colour of the "canvas" background. The colour may be given as
either a colour name or a comma separated triple of Red, Green, Blue (RGB)
components enclosed in square brackets. Typing the command help
colours will give a list of the predefined colour names recognised by
RasMol. When running under X Windows, RasMol also recognises colours in
the X server's colour name database.
- Set BondMode
- The RasMol set bondmode command controls the
mechanism used to select individual bonds and modifies the display of
bonded and non-bonded atoms by subsequent wireframe commands.
- Set Bonds
- The RasMol bonds parameter is used to control
display of double and triple bonds as multiple lines or cylinders.
Currently bond orders are only read from MDL Mol files, Sybyl Mol2 format
files, Tripos Alchemy format files, CIF and mmCIF, and suitable PDB files.
Double (and triple) bonds are specified in some PDB files by specifying a
given bond twice (and three times) in CONECT records. The command set
bonds on enables the display of bond orders, and the command set
bonds off disables them.
- Set BoundBox
- The RasMol boundbox parameter controls the display
of the current molecule's bounding box on the display. The bounding box is
orthogonal to the data file's original coordinate axes. The set
boundbox command is similar to the commands set axes and set
unitcell that display orthogonal coordinate axes and the bounding box,
respectively.
- Set Cartoon
- The RasMol cartoon parameter is used to control
display of the cartoon version of the ribbons display. By default,
the C-termini of beta-sheets are displayed as arrow heads. This may be
enabled and disabled using the set cartoons <boolean>
command. The depth of the cartoon may be adjusted using the cartoons
<number> command. The set cartoons command without any
parameters returns these two options to
their default values.
- Set CisAngle
- The RasMol cisangle parameter controls the cutoff
angle for identifying cis peptide
bonds. If no value is given, the cutoff is set to 90 degrees.
- Set Display
- This command controls the display mode within RasMol. By
default, set display normal, RasMol displays the molecule in the
representation specified by the user. The command set display
selected changes the display mode such that the molecule is
temporarily drawn so as to indicate currently selected portion of the
molecule. The user specified colour scheme and representation remains
unchanged. In this representation all selected atoms are shown in yellow
and all non selected atoms are shown in blue. The colour of the background
is also changed to a dark grey to indicate the change of display mode.
This command is typically only used by external Graphical User Interfaces
(GUIs).
- Set FontSize
- The RasMol set fontsize command is used to control
the size of the characters that form atom labels. This value corresponds
to the height of the displayed character in pixels. The maximum value of
fontsize is 48 pixels, and the default value is 8 pixels high.
Fixed or proportional spacing may be selected by appending the
"FS" or "PS" modifiers, respectively. The default is
"FS". To display atom labels on the screen use the RasMol
label command and to change the colour of displayed labels, use the
colour labels command.
- Set FontStroke
- The RasMol set fontstroke command is used to control
the size of the stroke width of the characters that form atom labels. This
value is the radius in pixels of cylinders used to form the strokes. The
special value of "0" is the default used for the normal single
pixel stroke width, which allows for rapid drawing and rotation of the
image. Non-zero values are provided to allow for more artistic atom labels
for publication at the expense of extra time in rendering the image.
- Set HBonds
- The RasMol hbonds parameter determines whether
hydrogen bonds are drawn between the donor and acceptor atoms of the
hydrogen bond, set hbonds sidechain or between the alpha carbon
atoms of the protein backbone and between the phosphorous atoms of the
nucleic acid backbone, set hbonds backbone. The actual display of
hydrogen bonds is controlled by the hbonds command. Drawing
hydrogen bonds between protein alpha carbons or nucleic acid phosphorous
atoms is useful when the rest of the molecule is shown in only a schematic
representation such as backbone, ribbons or strands.
This parameter is similar to the RasMol ssbonds parameter.
- Set Hetero
- The RasMol hetero parameter is used to modify the
'default' behaviour of the RasMol select command, i.e. the
behaviour of select without any parameters. When this value is
false, the default select region does not include any
heterogeneous atoms (refer to the predefined set hetero ). When
this value is true, the default select region may contain
hetero atoms. This parameter is similar to the RasMol hydrogen
parameter which determines whether hydrogen atoms should be included in
the default set. If both hetero and hydrogen are
true, select without any parameters is equivalent to
select all.
- Set HourGlass
- The RasMol hourglass parameter allows the user to
enable and disable the use of the 'hour glass' cursor used by RasMol to
indicate that the program is currently busy drawing the next frame. The
command set hourglass on enables the indicator, whilst set
hourglass off prevents RasMol from changing the cursor. This is useful
when spinning the molecule, running a sequence of commands from a script
file or using interprocess communication to execute complex sequences of
commands. In these cases a 'flashing' cursor may be distracting.
- Set Hydrogen
- The RasMol hydrogen parameter is used to modify the
"default" behaviour of the RasMol select command, i.e.
the behaviour of select without any parameters. When this value is
false, the default select region does not include any
hydrogen, deuterium or tritium atoms (refer to the predefined set
hydrogen ). When this value is true, the default
select region may contain hydrogen atoms. This parameter is similar
to the RasMol hetero parameter which determines whether
heterogeneous atoms should be included in the default set. If both
hydrogen and hetero are true, select without
any parameters is equivalent to select all.
- Set Kinemage
- The RasMol set kinemage command controls the amount
of detail stored in a Kinemage output file generated by the RasMol
write kinemage command. The output kinemage files are intended to
be displayed by David Richardson's Mage program. set kinemage
false, the default, only stores the currently displayed representation
in the generated output file. The command set kinemage true,
generates a more complex Kinemage that contains both the wireframe and
backbone representations as well as the coordinate axes, bounding box and
crystal unit cell.
- Set Menus
- The RasMol set menus command enables the canvas
window's menu buttons or menu bar. This command is typically only used by
graphical user interfaces or to create as large an image as possible when
using Microsoft Windows.
- Set Monitor
- The RasMol set monitor command enables
monitors. The distance monitor labels may be turned off with the
command set monitor off, and re-enabled with the command set
monitor on.
- Set Mouse
- The RasMol set mouse command sets the rotation,
translation, scaling and zooming mouse bindings. The default value is
rasmol which is suitable for two button mice (for three button mice
the second and third buttons are synonymous); X-Y rotation is controlled
by the first button, and X-Y translation by the second. Additional
functions are controlled by holding a modifier key on the keyboard.
[Shift] and the first button performs scaling, [shift] and the second
button performs Z-rotation, and [control] and the first mouse button
controls the clipping plane. The insight and quanta options
provide the same mouse bindings as other packages for experienced users.
- Set Picking
- The RasMol set picking series of commands affects
how a user may interact with a molecule displayed on the screen in RasMol.
- Set Play
- The RasMol set play.fps command gives the number of
frames per second for playback by the play command (default 24
frames per second).
- Set Radius
- The RasMol set radius command is used to alter the
behaviour of the RasMol dots command depending upon the value of
the solvent parameter. When solvent is true, the
radius parameter controls whether a true van der Waals' surface is
generated by the dots command. If the value of radius is
anything other than zero, that value is used as the radius of each atom
instead of its true vdW value. When the value of solvent is
true, this parameter determines the 'probe sphere' (solvent)
radius. The parameter may be given as an integer in rasmol units or
containing a decimal point in Angstroms. The default value of this
parameter is determined by the value of solvent and changing
solvent resets radius to its new default value.
- Set Record
- The RasMol set record.aps gives the maximum
on-screen velocity in Angstroms per second in animating translations,
rotations and zooms (default 10 A/second).
- Set ShadePower
- The shadepower parameter (adopted from RasTop)
determines the shade repartition (the contrast) used in rendering solid
objects. This value between 0 and 100 adjusts shading on an object surface
oriented along the direction to the light source. Changing the shadepower
parameter does not change the maximum or the minimum values of this
shading, as does changing the ambient parameter. A value of 100
concentrates the light on the top of spheres, giving a highly specular,
glassy rendering (see the specpower parameter). A value of 0
distributes the light on the entire object.
- Set Shadow
- The RasMol set shadow command enables and disables
ray-tracing of the currently rendered image. Currently only the
spacefilling representation is shadowed or can cast shadows. Enabling
shadowing will automatically disable the Z-clipping (slabbing) plane using
the command slab off. Ray-tracing typically takes about several
seconds for a moderately sized protein. It is recommended that shadowing
be normally disabled whilst the molecule is being transformed or
manipulated, and only enabled once an appropriate viewpoint is selected,
to provide a greater impression of depth.
- Set SlabMode
- The RasMol slabmode parameter controls the rendering
method of objects cut by the slabbing (z-clipping) plane. Valid slabmode
parameters are "reject", "half", "hollow",
"solid" and "section".
- Set Solvent
- The RasMol set solvent command is used to control
the behaviour of the RasMol dots command. Depending upon the value
of the solvent parameter, the dots command either generates
a van der Waals' or a solvent accessible surface around the currently
selected set of atoms. Changing this parameter automatically resets the
value of the RasMol radius parameter. The command set solvent
false, the default value, indicates that a van der Waals' surface
should be generated and resets the value of radius to zero. The
command set solvent true indicates that a 'Connolly' or 'Richards'
solvent accessible surface should be drawn and sets the radius
parameter, the solvent radius, to 1.2 Angstroms (or 300 RasMol units).
- Set Specular
- The RasMol set specular command enables and disables
the display of specular highlights on solid objects drawn by RasMol.
Specular highlights appear as white reflections of the light source on the
surface of the object. The current RasMol implementation uses an
approximation function to generate this highlight.
- Set SpecPower
- The specpower parameter determines the shininess of
solid objects rendered by RasMol. This value between 0 and 100 adjusts the
reflection coefficient used in specular highlight calculations. The
specular highlights are enabled and disabled by the RasMol set
specular command. Values around 20 or 30 produce plastic looking
surfaces. High values represent more shiny surfaces such as metals, while
lower values produce more diffuse/dull surfaces.
- Set SSBonds
- The RasMol ssbonds parameter determines whether
disulphide bridges are drawn between the sulphur atoms in the sidechain
(the default) or between the alpha carbon atoms in the backbone of the
cysteines residues. The actual display of disulphide bridges is controlled
by the ssbonds command. Drawing disulphide bridges between alpha
carbons is useful when the rest of the protein is shown in only a
schematic representation such as backbone, ribbons or
strands. This parameter is similar to the RasMol hbonds
parameter.
- Set Stereo
- The RasMol set stereo parameter controls the
separation between the left and right images. Turning stereo on and off
doesn't reposition the centre of the molecule.
- Set Strands
- The RasMol strands parameter controls the number of
parallel strands that are displayed in the ribbon representations of
proteins. The permissible values for this parameter are 1, 2, 3, 4, 5 and
9. The default value is 5. The number of strands is constant for all
ribbons being displayed. However, the ribbon width (the separation between
strands) may be controlled on a residue by residue basis using the RasMol
ribbons command.
- Set Transparent
- The RasMol transparent parameter controls the
writing of transparent GIFs by the write gif <filename>
command. This may be controlled by the set transparent on and
set transparent off commands.
- Set UnitCell
- The RasMol unitcell parameter controls the display
of the crystallographic unit cell on the current display. The crystal cell
is only enabled if the appropriate crystal symmetry information is
contained in the PDB, CIF or mmCIF data file. The RasMol command show
symmetry display details of the crystal's space group and unit cell
axes. The set unitcell command is similar to the commands set
axes and set boundbox that display orthogonal coordinate axes
and the bounding box, respectively.
- Set VectPS
- The RasMol vectps parameter is use to control the
way in which the RasMol write command generates vector PostScript
output files. The command set vectps on enables the use of black
outlines around spheres and cylinder bonds producing
"cartoon-like" high resolution output. However, the current
implementation of RasMol incorrectly cartoons spheres that are intersected
by more than one other sphere. Hence "ball and stick" models are
rendered correctly but not large spacefilling spheres models. Cartoon
outlines can be disabled, the default, by the command set vectps
off.
- Set Write
- The RasMol write parameter controls the use of the
save and write commands within scripts, but it may only be
executed from the command line. By default, this value is false,
prohibiting the generation of files in any scripts executed at start-up
(such as those launched from a WWW browser). However, animators may start
up RasMol interactively: type set write on and then execute a
script to generate each frame using the source command.
ATOM EXPRESSIONS¶
RasMol atom expressions uniquely identify an arbitrary group of atoms within a molecule. Atom expressions are composed of either primitive expressions, predefined sets, comparison operators, within expressions, or logical (boolean) combinations of the above expression types.- Primitive Expressions
- RasMol primitive expressions are the fundamental building
blocks of atom expressions. There are two types of primitive expression.
The first type is used to identify a given residue number or range of
residue numbers. A single residue is identified by its number (position in
the sequence), and a range is specified by lower and upper bounds
separated by a hyphen character. For example select 5,6,7,8 is also
select 5-8. Note that this selects the given residue numbers in all
macromolecule chains.
- Comparison Operators
- Parts of a molecule may also be distinguished using
equality, inequality and ordering operators on their properties. The
format of such comparison expression is a property name, followed by a
comparison operator and then an integer value.
- Within Expressions
- A RasMol within expression allows atoms to be
selected on their proximity to another set of atoms. A within
expression takes two parameters separated by a comma and surrounded by
parentheses. The first argument is an integer value called the
"cut-off" distance of the within expression and the second
argument is any valid atom expression. The cut-off distance is expressed
in either integer RasMol units or Angstroms containing a decimal point. An
atom is selected if it is within the cut-off distance of any of the atoms
defined by the second argument. This allows complex expressions to be
constructed containing nested within expressions.
- Predefined Sets
- RasMol atom expressions may contain predefined sets. These
sets are single keywords that represent portions of a molecule of
interest. Predefined sets are often abbreviations of primitive atom
expressions. In some cases the use of predefined sets allows selection of
areas of a molecule that could not otherwise be distinguished. A list of
the currently predefined sets is given below. In addition to the sets
listed here, RasMol also treats element names (and their plurals) as
predefined sets containing all atoms of that element type, i.e. the
command select oxygen is equivalent to the command select
elemno=8.
Predefined Sets¶
- AT Set
- This set contains the atoms in the complementary
nucleotides adenosine and thymidine (A and T, respectively). All
nucleotides are classified as either the set at or the set
cg This set is equivalent to the RasMol atom expressions
a,t, and nucleic and not cg.
- Acidic Set
- The set of acidic amino acids. These are the residue types
Asp and Glu. All amino acids are classified as either acidic,
basic or neutral. This set is equivalent to the
RasMol atom expressions asp, glu and amino and not (basic or
neutral).
- Acyclic Set
- The set of atoms in amino acids not containing a cycle or
ring. All amino acids are classified as either cyclic or
acyclic. This set is equivalent to the RasMol atom expression
amino and not cyclic.
- Aliphatic Set
- This set contains the aliphatic amino acids. These are the
amino acids Ala, Gly, Ile, Leu and Val. This set is equivalent to the
RasMol atom expression ala, gly, ile, leu, val.
- Alpha Set
- The set of alpha carbons in the protein molecule. This set
is approximately equivalent to the RasMol atom expression *.CA.
This command should not be confused with the predefined set helix
which contains the atoms in the amino acids of the protein's alpha
helices.
- Amino Set
- This set contains all the atoms contained in amino acid
residues. This is useful for distinguishing the protein from the nucleic
acid and heterogeneous atoms in the current molecule database.
- Aromatic Set
- The set of atoms in amino acids containing aromatic rings.
These are the amino acids His, Phe, Trp and Tyr. Because they contain
aromatic rings all members of this set are member of the predefined set
cyclic. This set is equivalent to the RasMol atom expressions
his, phe, trp, tyr and cyclic and not pro.
- Backbone Set
- This set contains the four atoms of each amino acid that
form the polypeptide N-C-C-O backbone of proteins, and the atoms of the
sugar phosphate backbone of nucleic acids. Use the RasMol predefined sets
protein and nucleic to distinguish between the two forms of
backbone. Atoms in nucleic acids and proteins are either backbone
or sidechain. This set is equivalent to the RasMol expression
(protein or nucleic) and not sidechain.
- Basic Set
- The set of basic amino acids. These are the residue types
Arg, His and Lys. All amino acids are classified as either acidic,
basic or neutral. This set is equivalent to the RasMol atom
expressions arg, his, lys and amino and not (acidic or
neutral).
- Bonded Set
- This set contain all the atoms in the current molecule
database that are bonded to at least one other atom.
- Buried Set
- This set contains the atoms in those amino acids that tend
(prefer) to be buried inside protein, away from contact with solvent
molecules. This set refers to the amino acids preference and not the
actual solvent accessibility for the current protein. All amino acids are
classified as either surface or buried. This set is
equivalent to the RasMol atom expression amino and not surface.
- CG Set
- This set contains the atoms in the complementary
nucleotides cytidine and guanosine (C and G, respectively). All
nucleotides are classified as either the set at or the set
cg This set is equivalent to the RasMol atom expressions c,g
and nucleic and not at.
- Charged Set
- This set contains the charged amino acids. These are the
amino acids that are either acidic or basic. Amino acids are
classified as being either charged or neutral. This set is
equivalent to the RasMol atom expressions acidic or basic and
amino and not neutral.
- Cyclic Set
- The set of atoms in amino acids containing a cycle or
rings. All amino acids are classified as either cyclic or
acyclic. This set consists of the amino acids His, Phe, Pro, Trp
and Tyr. The members of the predefined set aromatic are members of
this set. The only cyclic but non-aromatic amino acid is proline. This set
is equivalent to the RasMol atom expressions his, phe, pro, trp,
tyr and aromatic or pro and amino and not acyclic.
- Cystine Set
- This set contains the atoms of cysteine residues that form
part of a disulphide bridge, i.e. half cystines. RasMol automatically
determines disulphide bridges, if neither the predefined set
cystine nor the RasMol ssbonds command have been used since
the molecule was loaded. The set of free cysteines may be determined using
the RasMol atom expression cys and not cystine.
- Helix Set
- This set contains all atoms that form part of a protein
alpha helix as determined by either the PDB file author or Kabsch and
Sander's DSSP algorithm. By default, RasMol uses the secondary structure
determination given in the PDB file if it exists. Otherwise, it uses the
DSSP algorithm as used by the RasMol structure command.
- Hetero Set
- This set contains all the heterogeneous atoms in the
molecule. These are the atoms described by HETATM entries in the PDB file.
These typically contain water, cofactors and other solvents and ligands.
All hetero atoms are classified as either ligand or
solvent atoms. These heterogeneous solvent atoms are further
classified as either water or ions.
- Hydrogen Set
- This predefined set contains all the hydrogen, deuterium
and tritium atoms of the current molecule. This predefined set is
equivalent to the RasMol atom expression elemno=1.
- Hydrophobic Set
- This set contains all the hydrophobic amino acids. These
are the amino acids Ala, Leu, Val, Ile, Pro, Phe, Met and Trp. All amino
acids are classified as either hydrophobic or polar. This
set is equivalent to the RasMol atom expressions ala, leu, val, ile,
pro, phe, met, trp and amino and not polar.
- Ions Set
- This set contains all the heterogeneous phosphate and
sulphate ions in the current molecule data file. A large number of these
ions are sometimes associated with protein and nucleic acid structures
determined by X-ray crystallography. These atoms tend to clutter an image.
All hetero atoms are classified as either ligand or
solvent atoms. All solvent atoms are classified as either
water or ions.
- Large Set
- All amino acids are classified as either small,
medium or large. This set is equivalent to the RasMol atom
expression amino and not (small or medium).
- Ligand Set
- This set contains all the heterogeneous cofactor and ligand
moieties that are contained in the current molecule data file. This set is
defined to be all hetero atoms that are not solvent atoms.
Hence this set is equivalent to the RasMol atom expression hetero and
not solvent.
- Medium Set
- All amino acids are classified as either small,
medium or large. This set is equivalent to the RasMol atom
expression amino and not (large or small).
- Neutral Set
- The set of neutral amino acids. All amino acids are
classified as either acidic, basic or neutral. This
set is equivalent to the RasMol atom expression amino and not (acidic
or basic).
- Nucleic Set
- The set of all atoms in nucleic acids, which consists of
the four nucleotide bases adenosine, cytidine, guanosine and thymidine (A,
C, G and T, respectively). All neucleotides are classified as either
purine or pyrimidine. This set is equivalent to the RasMol
atom expressions a,c,g,t and purine or pyrimidine. The
symbols for RNA nucleotides (U, +U, I, 1MA, 5MC, OMC, 1MG, 2MG, M2G, 7MG,
OMG, YG, H2U, 5MU, and PSU) are also recognized as members of this set.
- Polar Set
- This set contains the polar amino acids. All amino acids
are classified as either hydrophobic or polar. This set is
equivalent to the RasMol atom expression amino and not hydrophobic.
- Protein Set
- The set of all atoms in proteins. This consists of the
RasMol predefined set amino and common post-translation
modifications.
- Purine Set
- The set of purine nucleotides. These are the bases
adenosine and guanosine (A and G, respectively). All nucleotides are
either purines or pyrimidines. This set is equivalent to the
RasMol atom expressions a,g and nucleic and not pyrimidine.
- Pyrimidine Set
- The set of pyrimidine nucleotides. These are the bases
cytidine and thymidine (C and T, respectively). All nucleotides are either
purines or pyrimidines. This set is equivalent to the RasMol
atom expressions c,t and nucleic and not purine.
- Selected Set
- This set contains the set of atoms in the currently
selected region. The currently selected region is defined by the preceding
select or restrict command and not the atom expression
containing the selected keyword.
- Sheet Set
- This set contains all atoms that form part of a protein
beta sheet as determined by either the PDB file author or Kabsch and
Sander's DSSP algorithm. By default, RasMol uses the secondary structure
determination given in the PDB file if it exists. Otherwise, it uses the
DSSP algorithm as used by the RasMol structure command.
- Sidechain Set
- This set contains the functional sidechains of any amino
acids and the base of each nucleotide. These are the atoms not part of the
polypeptide N-C-C-O backbone of proteins or the sugar phosphate backbone
of nucleic acids. Use the RasMol predefined sets protein and
nucleic to distinguish between the two forms of sidechain. Atoms in
nucleic acids and proteins are either backbone or sidechain.
This set is equivalent to the RasMol expression (protein or nucleic)
and not backbone.
- Small Set
- All amino acids are classified as either small,
medium or large. This set is equivalent to the RasMol atom
expression amino and not (medium or large).
- Solvent Set
- This set contains the solvent atoms in the molecule
coordinate file. These are the heterogeneous water molecules, phosphate
and sulphate ions. All hetero atoms are classified as either
ligand or solvent atoms. All solvent atoms are
classified as either water or ions. This set is equivalent
to the RasMol atom expressions hetero and not ligand and water
or ions.
- Surface Set
- This set contains the atoms in those amino acids that tend
(prefer) to be on the surface of proteins, in contact with solvent
molecules. This set refers to the amino acids preference and not the
actual solvent accessibility for the current protein. All amino acids are
classified as either surface or buried. This set is
equivalent to the RasMol atom expression amino and not buried.
- Turn Set
- This set contains all atoms that form part of a protein
turns as determined by either the PDB file author or Kabsch and Sander's
DSSP algorithm. By default, RasMol uses the secondary structure
determination given in the PDB file if it exists. Otherwise, it uses the
DSSP algorithm as used by the RasMol structure command.
- Water Set
- This set contains all the heterogeneous water molecules in
the current database. A large number of water molecules are sometimes
associated with protein and nucleic acid structures determined by X-ray
crystallography. These atoms tend to clutter an image. All hetero
atoms are classified as either ligand or solvent atoms. The
solvent atoms are further classified as either water or
ions.
- Set Summary
- The table below summarises RasMol's classification of the
common amino acids.
COLOUR SCHEMES¶
The RasMol colour command allows different objects (such as atoms, bonds and ribbon segments) to be given a specified colour. Typically this colour is either a RasMol predefined colour name or an RGB triple. Additionally RasMol also supports alt, amino, chain, charge, cpk, group, model, shapely, structure, temperature or user colour schemes for atoms, and hbond type colour scheme for hydrogen bonds and electrostatic potential colour scheme for dot surfaces. The 24 currently predefined colour names are Black, Blue, BlueTint, Brown, Cyan, Gold, Grey, Green, GreenBlue, GreenTint, HotPink, Magenta, Orange, Pink, PinkTint, Purple, Red, RedOrange, SeaGreen, SkyBlue, Violet, White, Yellow and YellowTint- Alt Colours
- The RasMol alt (Alternate Conformer) colour scheme
codes the base structure with one colour and applies a limited number of
colours to each alternate conformer. In a RasMol built for 8-bit colour
systems, 4 colours are allowed for alternate conformers. Otherwise, 8
colours are available.
- Amino Colours
- The RasMol amino colour scheme colours amino acids
according to traditional amino acid properties. The purpose of colouring
is to identify amino acids in an unusual or surprising environment. The
outer parts of a protein that are polar are visible (bright) colours and
non-polar residues darker. Most colours are hallowed by tradition. This
colour scheme is similar to the shapely scheme.
- Chain Colours
- The RasMol chain colour scheme assigns each
macromolecular chain a unique colour. This colour scheme is particularly
useful for distinguishing the parts of multimeric structure or the
individual 'strands' of a DNA chain. Chain can be selected from the
RasMol Colours menu.
- Charge Colours
- The RasMol charge colour scheme colour codes each
atom according to the charge value stored in the input file (or beta
factor field of PDB files). High values are coloured in blue (positive)
and lower values coloured in red (negative). Rather than use a fixed scale
this scheme determines the maximum and minimum values of the
charge/temperature field and interpolates from red to blue appropriately.
Hence, green cannot be assumed to be 'no net charge' charge.
- CPK Colours
- The RasMol cpk colour scheme is based upon the
colours of the popular plastic spacefilling models which were developed by
Corey, Pauling and later improved by Kultun. This colour scheme colours
'atom' objects by the atom (element) type. This is the scheme
conventionally used by chemists. The assignment of the most commonly used
element types to colours is given below.
- Group Colours
- The RasMol group colour scheme colour codes residues
by their position in a macromolecular chain. Each chain is drawn as a
smooth spectrum from blue through green, yellow and orange to red. Hence
the N terminus of proteins and 5' terminus of nucleic acids are coloured
red and the C terminus of proteins and 3' terminus of nucleic acids are
drawn in blue. If a chain has a large number of heterogeneous molecules
associated with it, the macromolecule may not be drawn in the full 'range'
of the spectrum. Group can be selected from the RasMol
Colours menu.
- NMR Model Colours
- The RasMol model colour scheme codes each NMR model
with a distinct colour. The NMR model number is taken as a numeric value.
High values are coloured in blue and lower values coloured in red. Rather
than use a fixed scale this scheme determines the maximum value of the NMR
model number and interpolates from red to blue appropriately.
- Shapely Colours
- The RasMol shapely colour scheme colour codes
residues by amino acid property. This scheme is based upon Bob
Fletterick's "Shapely Models". Each amino acid and nucleic acid
residue is given a unique colour. The shapely colour scheme is used
by David Bacon's Raster3D program. This colour scheme is similar to the
amino colour scheme.
- Structure Colours
- The RasMol structure colour scheme colours the
molecule by protein secondary structure. Alpha helices are coloured
magenta, [240,0,128], beta sheets are coloured yellow, [255,255,0], turns
are coloured pale blue, [96,128,255] and all other residues are coloured
white. The secondary structure is either read from the PDB file (HELIX,
SHEET and TURN records), if available, or determined using Kabsch and
Sander's DSSP algorithm. The RasMol structure command may be used
to force DSSP's structure assignment to be used.
- Temperature Colours
- The RasMol temperature colour scheme colour codes
each atom according to the anisotropic temperature (beta) value stored in
the PDB file. Typically this gives a measure of the mobility/uncertainty
of a given atom's position. High values are coloured in warmer (red)
colours and lower values in colder (blue) colours. This feature is often
used to associate a "scale" value [such as amino acid
variability in viral mutants] with each atom in a PDB file, and colour the
molecule appropriately.
- User Colours
- The RasMol user colour scheme allows RasMol to use
the colour scheme stored in the PDB file. The colours for each atom are
stored in COLO records placed in the PDB data file. This convention was
introduced by David Bacon's Raster3D program.
- HBond Type Colours
- The RasMol type colour scheme applies only to
hydrogen bonds, hence is used in the command colour hbonds type.
This scheme colour codes each hydrogen bond according to the distance
along a protein chain between hydrogen bond donor and acceptor. This
schematic representation was introduced by Belhadj-Mostefa and
Milner-White. This representation gives a good insight into protein
secondary structure (hbonds forming alpha helices appear red, those
forming sheets appear yellow and those forming turns appear magenta).
- Potential Colours
- The RasMol potential colour scheme applies only to
dot surfaces, hence is used in the command colour dots potential.
This scheme colours each currently displayed dot by the electrostatic
potential at that point in space. This potential is calculated using
Coulomb's law taking the temperature/charge field of the input file to be
the charge assocated with that atom. This is the same interpretation used
by the colour charge command. Like the charge colour scheme
low values are blue/white and high values are red.
- Amino Acid Codes
- The following table lists the names, single letter and
three letter codes of each of the amino acids.
- Booleans
- A boolean parameter is a truth value. Valid boolean values
are 'true' and 'false', and their synonyms 'on' and 'off'. Boolean
parameters are commonly used by RasMol to either enable or disable a
representation or option.
FILE FORMATS¶
Protein Data Bank Files- RasMol Interpretation of PDB fields
- Atoms located at 9999.000, 9999.000, 9999.000 are assumed
to be Insight pseudo atoms and are ignored by RasMol. Atom names beginning
' Q' are also assumed to be pseudo atoms or position markers.
- PDB Colour Scheme Specification
- RasMol also accepts the supplementary COLO record type in
the PDB files. This record format was introduced by David Bacon's Raster3D
program for specifying the colour scheme to be used when rendering the
molecule. This extension is not currently supported by the PDB. The COLO
record has the same basic record type as the ATOM and HETATM records
described above.
- Multiple NMR Models
- RasMol loads all of the NMR models from a PDB file no
matter which command is used: load pdb <filename> or load
nmrpdb <filename>
- CIF and mmCIF Format Files
- CIF is the IUCr standard for presentation of small
molecules and mmCIF is intended as the replacement for the fixed-field PDB
format for presentation of macromolecular structures. RasMol can accept
data sets in either format.
MACHINE-SPECIFIC SUPPORT¶
In the following sections, support for Monochrome X-Windows, Tcl/Tk IPC, UNIX sockets based IPC, Compiling RasWin with Borland and MetroWerks are described.- Monochrome X-Windows Support
- RasMol supports the many monochrome UNIX workstations
typically found in academia, such as low-end SUN workstations and NCD
X-terminals. The X11 version of RasMol (when compiled in 8 bit mode) now
detects black and white X-Windows displays and enables dithering
automatically. The use of run-time error diffusion dithering means that
all display modes of RasMol are available when in monochrome mode. For
best results, users should experiment with the set ambient command to
ensure the maximum contrast in resulting images.
- Tcl/Tk IPC support
- Version 4 of Tk graphics library changed the protocol used
to communicate between Tk applications. RasMol version 2.6 was modified
such that it could communicate with both this new protocol and the
previous version 3 protocol supported by RasMol v2.5. Although Tcl/Tk 3.x
applications may only communicate with other 3.x applications and Tcl/Tk
4.x applications with other 4.x applications, these changes allow RasMol
to communicate between processes with both protocols (potentially
concurrently).
- UNIX sockets based IPC
- The UNIX implementation of RasMol supports BSD-style socket
communication. An identical socket mechanism is also being developed for
VMS, Apple Macintosh and Microsoft Windows systems. This should allow
RasMol to interactively display results of a computation on a remote host.
The current protocol acts as a TCP/IP server on port 21069 that executes
command lines until either the command exit or the command
quit is typed. The command exit from the RasMol server, the command
quit both disconnects the current session and terminates RasMol.
This functionality may be tested using the UNIX command telnet
<hostname> 21069.
- Compiling RasWin with Borland and MetroWerks
- A number of changes were made to the source code in the
transition from version 2.5 to 2.6 to allow the Microsoft Windows version
of RasMol to compile using the Borland C/C++ compiler. These fixes include
name changes for the standard library and special code to avoid a bug in
_fmemset. Additional changes were made in the transition from 2.6 to 2.7
to allow compilation with the MetroWerks compilers.
BIBLIOGRAPHY¶
Molecular GraphicsSEE ALSO¶
The RasMol User Manual!AUTHOR¶
1992-1998 by Roger Sayle (rasmol@ggr.co.uk)July 2009 |