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README,
manual.doc,
manual.ps,
rasmol.0,
rasmol.1,
rasmol.hlp,
rasmol.html,
rasmol.txt,
rasmol.vms,
raswin.hpj,
raswin.rtf,
refcard.doc,
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RASMOL(1) User Commands RASMOL(1)
NNNNAAAAMMMMEEEE
rasmol - Molecular Graphics Visualisation Tool v2.5
SSSSYYYYNNNNOOOOPPPPSSSSIIIISSSS
rrrraaaassssmmmmoooollll [---- nnnnooooddddiiiippppllllaaaayyyy] [[ ---- _f_o_r_m_a_t ] _f_i_l_e_n_a_m_e] [ ---- ssssccccrrrriiiipppptttt
_s_c_r_i_p_t_f_i_l_e]
FFFFOOOORRRRMMMMAAAATTTTSSSS
----ppppddddbbbb Brookhaven Protein Databank
----mmmmddddllll MDL's MOL File Format
----mmmmoooollll2222 Tripos' Sybyl MOL2 Format
----xxxxyyyyzzzz MSC's XYZ (XMol) Format
----aaaallllcccchhhheeeemmmmyyyy Alchemy File Format
----cccchhhhaaaarrrrmmmmmmmm CHARMm File Format
DDDDEEEESSSSCCCCRRRRIIIIPPPPTTTTIIIIOOOONNNN
RasMol2 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
Microsoft Windows, Apple Macintosh, UNIX and VMS systems.
The UNIX and VMS systems require an 8, 24 or 32 bit colour X
Windows display (X11R4 or later). The program reads in a
molecule co-ordinate file and interactively displays the
molecule on the screen in a variety of colour schemes and
molecule representations. Currently available representa-
tions include depth-cued wireframes, 'Dreiding' sticks, spa-
cefilling (CPK) spheres, ball and stick, solid and strand
biomolecular ribbons, atom labels and dot surfaces.
CCCCOOOOMMMMMMMMAAAANNNNDDDDSSSS
RasMol allows the execution of interactive commands typed at
the RRRRaaaassssMMMMoooollll>>>> 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.
The commands/keywords currently recognised by RasMol are
given below.
BBBBaaaacccckkkkbbbboooonnnneeee
The RasMol bbbbaaaacccckkkkbbbboooonnnneeee command permits the representation
of a polypeptide backbone as a series of bonds connect-
ing 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 paramater the same as the
wwwwiiiirrrreeeeffffrrrraaaammmmeeee command. The command bbbbaaaacccckkkkbbbboooonnnneeee ooooffffffff turns off
Sun Microsystems Last change: October 1994 1
RASMOL(1) User Commands RASMOL(1)
the selected `bonds', and bbbbaaaacccckkkkbbbboooonnnneeee oooonnnn 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 ccccoooolllloooouuuurrrr bbbbaaaacccckkkkbbbboooonnnneeee command.
BBBBaaaacccckkkkggggrrrroooouuuunnnndddd
The RasMol bbbbaaaacccckkkkggggrrrroooouuuunnnndddd 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 hhhheeeellllpppp ccccoooolllloooouuuurrrrssss 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 data-
base.
The bbbbaaaacccckkkkggggrrrroooouuuunnnndddd command is synonymous with the RasMol
sssseeeetttt bbbbaaaacccckkkkggggrrrroooouuuunnnndddd command.
CCCCeeeennnnttttrrrreeee
The RasMol cccceeeennnnttttrrrreeee command defines the point about which
the rrrroooottttaaaatttteeee command and the scroll bars rotate the
current molecule. Without a parameter the centre com-
mand 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 expres-
sion. Hence, if a single atom is specified by the
expression, that atom will remain `stationary' during
rotations.
Type hhhheeeellllpppp eeeexxxxpppprrrreeeessssssssiiiioooonnnn for more information on RasMol
atom expressions.
CCCClllliiiippppbbbbooooaaaarrrrdddd
The RasMol cccclllliiiippppbbbbooooaaaarrrrdddd command places a copy of the
currently displayed image on the local graphics `clip-
board'. Note: this command is not yet supported on UNIX
or VMS machines. It is intended to make transfering
images between applications easier under Microsoft Win-
dows or on an Apple Macintosh.
When using RasMol on a UNIX or VMS system this func-
tionality may be achieved by generating a raster image
in a format that can be read by the receiving program
using the RasMol wwwwrrrriiiitttteeee command.
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RASMOL(1) User Commands RASMOL(1)
CCCCoooolllloooouuuurrrr
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 hhhheeeellllpppp ccccoooolllloooouuuurrrrssss will give a list of all the
predefined colour names recognised by RasMol.
Allowed objects are aaaattttoooommmmssss,,,, bbbboooonnnnddddssss,,,, bbbbaaaacccckkkkbbbboooonnnneeee,,,, rrrriiiibbbbbbbboooonnnnssss
llllaaaabbbbeeeellllssss ddddoooottttssss,,,, hhhhbbbboooonnnnddddssss,,,, and ssssssssbbbboooonnnnddddssss.... If no object is
specified, the default keyword aaaattttoooommmm is assumed. Some
colour schemes are defined for certain object types.
The colour scheme nnnnoooonnnneeee can be applied all objects
accept atoms and dots, stating that the selected
objects have no colour of their own, but use the colour
of their associated atoms (i.e. the atoms they con-
nect). AAAAttttoooommmm objects can also be coloured by ccccppppkkkk,,,,
aaaammmmiiiinnnnoooo,,,, cccchhhhaaaaiiiinnnn,,,, ggggrrrroooouuuupppp,,,, sssshhhhaaaappppeeeellllyyyy,,,, ssssttttrrrruuuuccccttttuuuurrrreeee,,,, tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee
cccchhhhaaaarrrrggggeeee and uuuusssseeeerrrr.... HHHHyyyyddddrrrrooooggggeeeennnn bbbboooonnnnddddssss ccccaaaannnn aaaallllssssoooo bbbbeeee ttttyyyyppppeeee and
dot surfaces can also be coloured by eeeelllleeeeccccttttrrrroooossssttttaaaattttiiiicccc
ppppooootttteeeennnnttttiiiiaaaallll.... For more information type hhhheeeellllpppp ccccoooolllloooouuuurrrr
<<<>>>....
CCCCoooonnnnnnnneeeecccctttt
The RasMol ccccoooonnnnnnnneeeecccctttt 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 ccccoooonnnnnnnneeeecccctttt
ffffaaaallllsssseeee uses an extremely fast heuristic algorithmm that
is suitable for determing bonding in large bio-
molecules such as proteins and nucleic acids. The com-
mand ccccoooonnnnnnnneeeecccctttt ttttrrrruuuueeee uses a slower more accurate algorithm
based upon covalent radii that is more suitable for
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 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 llllooooaaaadddd command.
DDDDeeeeffffiiiinnnneeee
The RasMol ddddeeeeffffiiiinnnneeee 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 expres-
sion defining them depends on the current transforma-
tion and representation of the molecule.
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RASMOL(1) User Commands RASMOL(1)
DDDDoooottttssss The RasMol ddddoooottttssss command is used to generate a Van der
Waal's 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
Waal's radius of any other atom (selected or not) are
not displayed. The command ddddoooottttssss oooonnnn deletes any exist-
ing dot surface and generates a dots surface around the
currently selected atom set with a default dot density
of 100. The command ddddoooottttssss ooooffffffff 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.
By default, the colour of each point on a dot surface
is the colour of it's closest atom at the time the sur-
face is generated. The colour of the whole dot surface
may be changed using the ccccoooolllloooouuuurrrr ddddoooottttssss command.
EEEEcccchhhhoooo The RasMol eeeecccchhhhoooo command is used to display a message in
the RasMol command/terminal window. The string parame-
ter may optionally be delimited in double quote charac-
ters. If no parameter is specified, the eeeecccchhhhoooo command
displays a blank line. This command is particularly
useful for displaying text from within a RasMol ssssccccrrrriiiipppptttt
file.
HHHHBBBBoooonnnnddddssss
The RasMol hhhhbbbboooonnnndddd 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 hhhhbbbboooonnnndddd 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 hhhhbbbboooonnnnddddssss oooonnnn
displays the selected `bonds' as dotted lines, and the
hhhhbbbboooonnnnddddssss ooooffffffff turns off their display. The colour of hbond
objects may be changed by the ccccoooolllloooouuuurrrr hhhhbbbboooonnnndddd command.
Initially, each hydrogen bond has the colours of its
connected atoms.
By default the dotted lines are drawn between the
accepting oxygen and the donating nitrogen. By using
the sssseeeetttt hhhhbbbboooonnnnddddssss command the alpha carbon positions of
the appropriate residues may be used instead. This is
especially useful when examining proteins in backbone
representation.
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RASMOL(1) User Commands RASMOL(1)
HHHHeeeellllpppp The RasMol hhhheeeellllpppp command provides on-line help on the
given topic.
LLLLaaaabbbbeeeellll
The RasMol llllaaaabbbbeeeellll 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 charac-
ter specifying the property to be displayed. An actual
'%' character may be displayed by using the expansion
specifier `%%'.
Atom labelling for the currently selected atoms may be
turned off with the command llllaaaabbbbeeeellll ooooffffffff.... By default, if
no string is given as a parameter RasMol uses labels
appropriate for the current molecule.
The colour of each label may be changed using the
ccccoooolllloooouuuurrrr llllaaaabbbbeeeellll command. By default, each label is drawn
in the same colour as the atom to which it is attached.
The size of the displayed text may be changed using the
sssseeeetttt ffffoooonnnnttttssssiiiizzzzeeee command.
LLLLooooaaaadddd Load a molecule co-ordinate file into RasMol2. Valid
molecule file formats are ppppddddbbbb (Brookhaven Protein Data-
bank), mmmmddddllll (Molecular Design Limited's MOL file for-
mat), aaaallllcccchhhheeeemmmmyyyy (Tripos' Alchemy file format), mmmmoooollll2222 (Tri-
pos' Sybyl Mol2 file format), cccchhhhaaaarrrrmmmmmmmm (CHARMm file for-
mat) or xxxxyyyyzzzz (MSC's XMol XYZ file format). If no file
format is specified, ppppddddbbbb is assumed by default. Only a
single molecule may be loaded at a time. To delete a
molecule prior to loading another use the RasMol zzzzaaaapppp
command.
The llllooooaaaadddd command selects all the atoms in the molecule,
centres it on the screen and renders it as a CPK
coloured wireframe model. If the molecule contains no
bonds (i.e. contains only alpha carbons), it is drawn
as an alpha carbon backbone. If the file specifies less
bonds than atoms, RasMol determines connectivity using
the ccccoooonnnnnnnneeeecccctttt command.
PPPPrrrriiiinnnntttt
The RasMol pppprrrriiiinnnntttt 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
Sun Microsystems Last change: October 1994 5
RASMOL(1) User Commands RASMOL(1)
take advantage of Microsoft Windows and Apple Macintosh
printer drivers. For example, allowing images to be
printed directly on a dot matrix printer.
When using RasMol on a UNIX or VMS system this func-
tionality may be achieved by either generating a
PostScript file using the RasMol wwwwrrrriiiitttteeee ppppssss or wwwwrrrriiiitttteeee
vvvveeeeccccttttppppssss commands and printing that or generating a ras-
ter image file and using a utility to dump that to the
local printer.
QQQQuuuuiiiitttt Exit from the RasMol program. The RasMol commands eeeexxxxiiiitttt
and qqqquuuuiiiitttt are synonymous.
RRRReeeennnnuuuummmmbbbbeeeerrrr
The RasMol rrrreeeennnnuuuummmmbbbbeeeerrrr 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 pro-
teins, 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 3' ter-
minus. All chains in the current database are renum-
bered and gaps in the original sequence are ignored.
The starting value for numbering may be negative.
RRRReeeesssseeeetttt
The RasMol rrrreeeesssseeeetttt command restores the original viewing
transformation and centre of rotation. The scale is set
to it default value, zzzzoooooooommmm 111100000000,,,, the centre of rotation
is set to the geometric centre of the currently loaded
molecule, cccceeeennnnttttrrrreeee aaaallllllll,,,, this centre is translated to the
middle of the screen and the viewpoint set to the
default orientation.
This command should not be mistaken for the RasMol zzzzaaaapppp
command which deletes the currently stored molecule,
returning the program to its initial state.
RRRReeeessssttttrrrriiiicccctttt
The RasMol rrrreeeessssttttrrrriiiicccctttt 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
effect only the currently selected region. The parame-
ter of a rrrreeeessssttttrrrriiiicccctttt command is a RasMol atom expression
that is evaluated for every atom of the current
Sun Microsystems Last change: October 1994 6
RASMOL(1) User Commands RASMOL(1)
molecule. This command is very similar to the RasMol
sssseeeelllleeeecccctttt command, except restrict disables the wwwwiiiirrrreeeeffffrrrraaaammmmeeee,,,,
ssssppppaaaacccceeeeffffiiiillllllll and bbbbaaaacccckkkkbbbboooonnnneeee representations in the non-
selected region.
Type "help expression" for more information on RasMol
atom expressions.
RRRRiiiibbbbbbbboooonnnnssss
The RasMol rrrriiiibbbbbbbboooonnnnssss command displays the currently
loaded protein or nucleic acid as a smooth solid "rib-
bon" 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 ccccoooolllloooouuuurrrr rrrriiiibbbbbbbboooonnnn command. If the
current ribbon colour is nnnnoooonnnneeee (the default), the colour
is taken from the alpha carbon at each position along
its length.
The width of the ribbon at each position is determined
by the optional parameter in the usual RasMol units. By
default the width of the ribbon is taken from the
secondary structure of the protein or a constant value
of 720 (2.88 Angstroms) for nucleic acids. The default
width of protein alpha helices and beta sheets is 380
(1.52 Angstroms) and 100 (0.4 Angstroms) for turns and
random coil. The secondary structure assignment is
either from the PDB file or calculated using the DSSP
algorithm as used by the ssssttttrrrruuuuccccttttuuuurrrreeee command. This com-
mand is similar to the RasMol command ssssttttrrrraaaannnnddddssss which
renders the biomolecular ribbon as parallel depth-cued
curves.
RRRRoooottttaaaatttteeee
Rotate the molecule about the specified axis. Permited
values for the axis parameter are "x", "y" and "z".
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.
SSSSaaaavvvveeee Save the currently selected set of atoms in either a
Brookhaven Protein Database (PDB) or Alchemy(tm) format
file. The distinction between this command and the
RasMol wwwwrrrriiiitttteeee command has been dropped. The only differ-
ence is that without a format specifier the ssssaaaavvvveeee com-
mand generates a PPPPDDDDBBBB file and the wwwwrrrriiiitttteeee command
Sun Microsystems Last change: October 1994 7
RASMOL(1) User Commands RASMOL(1)
generates a GGGGIIIIFFFF image.
SSSSccccrrrriiiipppptttt
The RasMol ssssccccrrrriiiipppptttt command reads a set of RasMol com-
mands 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 max-
imum "depth" of 10, allowing compilicated 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 eeeecccchhhhoooo command.
The most common way to generate a RasMol script file is
to use the wwwwrrrriiiitttteeee ssssccccrrrriiiipppptttt or wwwwrrrriiiitttteeee rrrraaaassssmmmmoooollll commands to
output the sequence of commands that are needed to
regenerate the current view, representation and colour-
ing of the currently displayed molecule.
The RasMol command ssssoooouuuurrrrcccceeee is synonymous with the ssssccccrrrriiiipppptttt
command.
SSSSeeeelllleeeecccctttt
Define the currently selected region of the molecule.
All subsequent RasMol commands that manipulate a
molecule or modify its colour or representation, only
effects the currently selected region. The parameter of
a sssseeeelllleeeecccctttt 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
sssseeeelllleeeecccctttt aaaallllllll.... The behaviour of the sssseeeelllleeeecccctttt command without
any parameters is determined by the RasMol hhhheeeetttteeeerrrroooo and
hhhhyyyyddddrrrrooooggggeeeennnn parameters.
Type "help expression" for more information on RasMol
atom expressions.
SSSSeeeetttt The RasMol sssseeeetttt 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, ommiting the
paramter option resets that parameter to its default
value. A list of valid parameter names is given below.
SSSShhhhoooowwww The RasMol sssshhhhoooowwww command display details of the status
Sun Microsystems Last change: October 1994 8
RASMOL(1) User Commands RASMOL(1)
of the currently loaded molecule. The command sssshhhhoooowwww
iiiinnnnffffoooorrrrmmmmaaaattttiiiioooonnnn 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 sssshhhhoooowwww sssseeeeqqqquuuueeeennnncccceeee lists
the residues that compose each chain of the molecule.
SSSSllllaaaabbbb The RasMol ssssllllaaaabbbb 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. 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.
SSSSppppaaaacccceeeeffffiiiillllllll
The RasMol ssssppppaaaacccceeeeffffiiiillllllll 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, ssssppppaaaa----
cccceeeeffffiiiillllllllllll ttttrrrruuuueeee,,,, the default, represents each atom as a
sphere of Van der Waals radius. The command ssssppppaaaacccceeeeffffiiiillllllll
ooooffffffff 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.
The tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee option sets the radius of each sphere
to the value stored in its temperature field. Zero or
negative values causes have no effect and values
greater than 2.0 are truncated to 2. The uuuusssseeeerrrr option
allows the radius of each spheres to be specified by
additional lines in the molecule's PDB file using Ras-
ter 3D's COLOR record extension.
The RasMol command ccccppppkkkk is synonymous with the ssssppppaaaacccceeeeffffiiiillllllll
command.
SSSSSSSSBBBBoooonnnnddddssss
The RasMol ssssssssbbbboooonnnnddddssss command is used to represent the
disulphide bridges of the protein molecule as either
dotted lines or cylinders between the connected cys-
teines. The first time that the ssssssssbbbboooonnnnddddssss command is
used, the program searches the structure of the protein
Sun Microsystems Last change: October 1994 9
RASMOL(1) User Commands RASMOL(1)
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 ssssssssbbbboooonnnnddddssss oooonnnn
displays the selected `bonds' as dotted lines, and the
command ssssssssbbbboooonnnnddddssss ooooffffffff 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 sssseeeetttt bbbboooonnnnddddmmmmooooddddeeee command. The
colour of disulphide bonds may be changed using the
ccccoooolllloooouuuurrrr ssssssssbbbboooonnnnddddssss command. By default, each disulphide
bond has the colours of its connected atoms.
By default disulphide bonds are drawn between the sul-
phur atoms within the cysteine groups. By using the sssseeeetttt
ssssssssbbbboooonnnnddddssss command the position of the cysteine's alpha
carbons may be used instead.
SSSSttttrrrraaaannnnddddssss
The RasMol ssssttttrrrraaaannnnddddssss 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
ccccoooolllloooouuuurrrr rrrriiiibbbbbbbboooonnnn command. If the current ribbon colour is
nnnnoooonnnneeee (the default), the colour is taken from the alpha
carbon at each position along its length. The colour of
the central and outermost strands may be coloured
independently using the ccccoooolllloooouuuurrrr rrrriiiibbbbbbbboooonnnn1111 and ccccoooolllloooouuuurrrr rrrriiiibbbb----
bbbboooonnnn2222 commands respectively. The number of strands in
the ribbon may be altered using the RasMol sssseeeetttt ssssttttrrrraaaannnnddddssss
command.
The width of the ribbon at each position is determined
by the optional parameter in the usual RasMol units. By
default the width of the ribbon is taken from the
secondary structure of the protein or a constant value
of 720 for nucleic acids (which produces a ribbon 2.88
Angstroms wide). The default width of protein alpha
helices and beta sheets is 380 (1.52 Angstroms) and 100
(0.4 Angstroms) for turns and random coil. The secon-
dary structure assignment is either from the PDB file
or calculated using the DSSP algorithm as used by the
ssssttttrrrruuuuccccttttuuuurrrreeee command. This command is similar to the
RasMol command rrrriiiibbbbbbbboooonnnnssss which renders the biomolecular
ribbon as a smooth shaded surface.
SSSSttttrrrruuuuccccttttuuuurrrreeee
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RASMOL(1) User Commands RASMOL(1)
The RasMol ssssttttrrrruuuuccccttttuuuurrrreeee command calculates secondary
structure assignments for the currently loaded protein.
If the original PDB file contained structural assign-
ment records (HELIX and SHEET) these are discarded.
Initially, the hydrogen bonds of the current molecule
are found, if this hasn't been done already. The secon-
dary structure is the determined using Kabsch and
Sander's DSSP algorithm. Once finished the program
reports the number of helices, strands and turns found.
TTTTrrrraaaannnnssssllllaaaatttteeee
The RasMol ttttrrrraaaannnnssssllllaaaatttteeee command moves the position of the
centre of the molecule on the screen. The axis parame-
ter 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. Permited 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" displace-
ment moves the molecule to the right, and a positive
"y" displacement moves the molecule down the screen.
The pair of commands ttttrrrraaaannnnssssllllaaaatttteeee xxxx 0000 and ttttrrrraaaannnnssssllllaaaatttteeee yyyy 0000
centres the molecule on the screen.
WWWWiiiirrrreeeeffffrrrraaaammmmeeee
The RasMol wwwwiiiirrrreeeeffffrrrraaaammmmeeee command represents each bond
within the selected region of the molecule as either a
cylinder, a line or 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
wwwwiiiirrrreeeeffffrrrraaaammmmeeee or wwwwiiiirrrreeeeffffrrrraaaammmmeeee oooonnnn.... 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
ccccoooolllloooouuuurrrr bbbboooonnnnddddssss command.
WWWWrrrriiiitttteeee
Write the current image to a file in a standard raster
format. Currently supported image file formats include
ggggiiiiffff (Compuserve GIF), ppppppppmmmm (Portable Pixmap), rrrraaaassss (Sun
rasterfile), ppppssss and eeeeppppssssffff (Encapsulated PostScript),
mmmmoooonnnnooooppppssss (Monochrome Encapsulated PostScript), bbbbmmmmpppp
(Microsoft bitmap) and ppppiiiicccctttt (Apple PICT). The wwwwrrrriiiitttteeee
command may also be used to generate command scripts
for other graphics programs. The format ssssccccrrrriiiipppptttt writes
out a file containing the RasMol ssssccccrrrriiiipppptttt commands to
Sun Microsystems Last change: October 1994 11
RASMOL(1) User Commands RASMOL(1)
reproduce the current image. The format mmmmoooollllssssccccrrrriiiipppptttt
writes out the commands required to render the current
view of the molecule as ribbons in Per Kraulis' Mol-
script program and the format kkkkiiiinnnneeeemmmmaaaaggggeeee the commands for
David Richardson's program Mage.
The distinction between this command and the RasMol
ssssaaaavvvveeee command has been dropped. The only difference is
that without a format specifier the ssssaaaavvvveeee command gen-
erates a PPPPDDDDBBBB file and the wwwwrrrriiiitttteeee command generates a GGGGIIIIFFFF
image.
ZZZZaaaapppp Deletes the contents of the current database and resets
parameter variables to their initial default state.
ZZZZoooooooommmm Change the magnification of the currently displayed
image. Boolean parameters either magnify or reset the
scale of current molecule. An integer parameter between
10 and 200 specifies the desired magnification as a
percentage of the default scale.
SSSSEEEETTTT PPPPAAAARRRRAAAAMMMMEEEETTTTEEEERRRRSSSS
RasMol has a number of internal parameters that may be modi-
fied using the sssseeeetttt command. These parameters control a
number of program options such as rendering options and
mouse button mappings.
SSSSeeeetttt AAAAmmmmbbbbiiiieeeennnntttt
The RasMol aaaammmmbbbbiiiieeeennnntttt parameter is used to control the
amount of ambient (or surrounding) light in the scene.
The aaaammmmbbbbiiiieeeennnntttt value must be between 0 and 100 that con-
trols 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 sha-
dow. For depth-cued objects this is the intensity of
objects furthest from the viewer.
This parameter is commonly used to correct for monitors
with different "gamma values" (brightness), to change
how light or dark a hardcopy image appears when printed
or to alter the feeling of depth for wireframe or rib-
bon representations.
SSSSeeeetttt AAAAxxxxeeeessss
The RasMol aaaaxxxxeeeessss parameter controls the display of
orthogonal co-ordinate axes on the current display. The
co-ordinate axes are those used in the molecule data
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RASMOL(1) User Commands RASMOL(1)
file, and the origin is the centre of the molecule's
bounding box. The sssseeeetttt aaaaxxxxeeeessss command is similar the the
commands sssseeeetttt bbbboooouuuunnnnddddbbbbooooxxxx and sssseeeetttt uuuunnnniiiittttcccceeeellllllll that display the
bounding box and the crystallographic unit cell respec-
tively.
SSSSeeeetttt BBBBaaaacccckkkkggggrrrroooouuuunnnndddd
The RasMol bbbbaaaacccckkkkggggrrrroooouuuunnnndddd 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 tri-
ple of Red, Green, Blue (RGB) components enclosed in
square brackets. Typing the command hhhheeeellllpppp ccccoooolllloooouuuurrrrssss 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 data-
base.
The command sssseeeetttt bbbbaaaacccckkkkggggrrrroooouuuunnnndddd is synonymous with the
RasMol command bbbbaaaacccckkkkggggrrrroooouuuunnnndddd....
SSSSeeeetttt BBBBoooonnnnddddMMMMooooddddeeee
The RasMol sssseeeetttt bbbboooonnnnddddmmmmooooddddeeee command controls the mechanism
used to select individual bonds. When using the sssseeeelllleeeecccctttt
and rrrreeeessssttttrrrriiiicccctttt commands, a given bond will be selected if
i) the bondmode is oooorrrr and either of the connected atoms
is selected, or ii) the bondmode is aaaannnndddd and both atoms
connected by the bond are selected. Hence an individual
bond may be uniquely identified by using the command
sssseeeetttt bbbboooonnnnddddmmmmooooddddeeee aaaannnndddd and then uniquely selecting the atoms
at both ends.
SSSSeeeetttt BBBBoooouuuunnnnddddBBBBooooxxxx
The RasMol bbbboooouuuunnnnddddbbbbooooxxxx parameter controls the display of
the current molecules bounding box on the display. The
bounding box is orthogonal to the data file's original
co-ordinate axes. The sssseeeetttt bbbboooouuuunnnnddddbbbbooooxxxx command is similar
the the commands sssseeeetttt aaaaxxxxeeeessss and sssseeeetttt uuuunnnniiiittttcccceeeellllllll that display
orthogonal co-ordinate axes and the bounding box
respectively.
SSSSeeeetttt DDDDiiiissssppppllllaaaayyyy
This command controls the display mode within RasMol.
By default, sssseeeetttt ddddiiiissssppppllllaaaayyyy nnnnoooorrrrmmmmaaaallll,,,, RasMol displays the
molecule in the representation specified by the user.
The command sssseeeetttt ddddiiiissssppppllllaaaayyyy sssseeeelllleeeecccctttteeeedddd 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
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RASMOL(1) User Commands RASMOL(1)
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).
SSSSeeeetttt HHHHBBBBoooonnnnddddssss
The RasMol hhhhbbbboooonnnnddddssss parameter determines whether hydrogen
bonds are drawn between the donor and acceptor atoms of
the hydrogen bond, sssseeeetttt hhhhbbbboooonnnnddddssss ssssiiiiddddeeeecccchhhhaaaaiiiinnnn or between the
alpha carbon atoms of the protein backbone and between
the phosphorous atoms of the nucleic acid backbone, sssseeeetttt
hhhhbbbboooonnnnddddssss bbbbaaaacccckkkkbbbboooonnnneeee.... The actual display of hydrogen bonds
is controlled by the hhhhbbbboooonnnnddddssss 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 bbbbaaaacccckkkkbbbboooonnnneeee,,,, rrrriiiibbbbbbbboooonnnnssss or ssssttttrrrraaaannnnddddssss.... his parameter is
similar to the RasMol ssssssssbbbboooonnnnddddssss parameter.
SSSSeeeetttt FFFFoooonnnnttttSSSSiiiizzzzeeee
The RasMol sssseeeetttt ffffoooonnnnttttssssiiiizzzzeeee command is used to control the
size of the characters that form atom labels. This
value corresponds to the height of the displayed char-
acter in pixels. The maximum value of ffffoooonnnnttttssssiiiizzzzeeee is 32
pixels, and the default value is 8 pixels high. To
display atom labels on the screen use the RasMol llllaaaabbbbeeeellll
command and to change the colour of displayed labels,
use the ccccoooolllloooouuuurrrr llllaaaabbbbeeeellllssss command.
SSSSeeeetttt HHHHeeeetttteeeerrrroooo
The RasMol hhhheeeetttteeeerrrroooo parameter is used to modify the
`default' behaviour of the RasMol sssseeeelllleeeecccctttt command, i.e.
the behaviour of sssseeeelllleeeecccctttt without any parameters. When
this value is ffffaaaallllsssseeee,,,, the default sssseeeelllleeeecccctttt region does not
include an heterogenous atoms (refer to the predefined
set hhhheeeetttteeeerrrroooo ). When this value is ttttrrrruuuueeee,,,, the default
sssseeeelllleeeecccctttt region may contain hetero atoms. This parameter
is similar to the RasMol hhhhyyyyddddrrrrooooggggeeeennnn parameter which
determines whether hydrogen atoms should be included in
the default set. If both hhhheeeetttteeeerrrroooo and hhhhyyyyddddrrrrooooggggeeeennnn are ttttrrrruuuueeee,,,,
sssseeeelllleeeecccctttt without any parameters is equivalent to sssseeeelllleeeecccctttt
aaaallllllll....
SSSSeeeetttt HHHHoooouuuurrrrGGGGllllaaaassssssss
The RasMol hhhhoooouuuurrrrggggllllaaaassssssss parameter allows the user to
enable and disable the use of the `hour glass' cursor
Sun Microsystems Last change: October 1994 14
RASMOL(1) User Commands RASMOL(1)
used by RasMol to indicate that the program is
currently busy drawing the next frame. The command sssseeeetttt
hhhhoooouuuurrrrggggllllaaaassssssss oooonnnn enable the indicator, whilst sssseeeetttt hhhhoooouuuurrrrggggllllaaaassssssss
ooooffffffff 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.
SSSSeeeetttt HHHHyyyyddddrrrrooooggggeeeennnn
The RasMol hhhhyyyyddddrrrrooooggggeeeennnn parameter is used to modify the
`default' behaviour of the RasMol sssseeeelllleeeecccctttt command, i.e.
the behaviour of sssseeeelllleeeecccctttt without any parameters. When
this value is ffffaaaallllsssseeee,,,, the default sssseeeelllleeeecccctttt region does not
include any hydrogen or deuterium atoms (refer to the
predefined set hhhhyyyyddddrrrrooooggggeeeennnn ). When this value is ttttrrrruuuueeee,,,, the
default sssseeeelllleeeecccctttt region may contain hydrogen atoms. This
parameter is similar to the RasMol hhhheeeetttteeeerrrroooo parameter
which determines whether heterogenous atoms should be
included in the default set. If both hhhhyyyyddddrrrrooooggggeeeennnn and
hhhheeeetttteeeerrrroooo are ttttrrrruuuueeee,,,, sssseeeelllleeeecccctttt without any parameters is
equivalent to sssseeeelllleeeecccctttt aaaallllllll....
SSSSeeeetttt KKKKiiiinnnneeeemmmmaaaaggggeeee
The RasMol sssseeeetttt kkkkiiiinnnneeeemmmmaaaaggggeeee command controls the amount of
detail stored in a Kinemage output file generated by
the RasMol wwwwrrrriiiitttteeee kkkkiiiinnnneeeemmmmaaaaggggeeee command. The output kinemage
files are intended to be displayed by David
Richardson's Mage program. sssseeeetttt kkkkiiiinnnneeeemmmmaaaaggggeeee ffffaaaallllsssseeee,,,, the
default, only stores the currently displayed represen-
tation in the generated output file. The command sssseeeetttt
kkkkiiiinnnneeeemmmmaaaaggggeeee ttttrrrruuuueeee,,,, generates a more complex Kinemage that
contains both the wireframe and backbone representa-
tions as well as the co-ordinate axes, bounding box and
crystal unit cell.
SSSSeeeetttt MMMMeeeennnnuuuussss
The RasMol sssseeeetttt mmmmeeeennnnuuuussss command enables the canvas
window's menu buttons or menu bar. This command is typ-
ically only used by graphical user interfaces or to
create as large as image as possible when using Micro-
soft Windows.
SSSSeeeetttt MMMMoooouuuusssseeee
The RasMol sssseeeetttt mmmmoooouuuusssseeee command sets the rotation, trans-
lation, scaling and zooming mouse bindings. The default
value is rrrraaaassssmmmmoooollll which is suitable for two button mice
(for three button mice the second and third buttons are
Sun Microsystems Last change: October 1994 15
RASMOL(1) User Commands RASMOL(1)
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 con-
trols the clipping plane. The iiiinnnnssssiiiigggghhhhtttt and qqqquuuuaaaannnnttttaaaa pro-
vide the same mouse bindings as other packages for
experienced users.
SSSSeeeetttt RRRRaaaaddddiiiiuuuussss
The RasMol sssseeeetttt rrrraaaaddddiiiiuuuussss command is used to alter the
behaviour of the RasMol ddddoooottttssss command depending upon the
value of the ssssoooollllvvvveeeennnntttt parameter. When ssssoooollllvvvveeeennnntttt is ttttrrrruuuueeee,,,,
the rrrraaaaddddiiiiuuuussss parameter controls whether a true Van der
Waal's surface is generated by the ddddoooottttssss command. If the
value of rrrraaaaddddiiiiuuuussss is anything other than zero, that value
is used as the radius of each atom instead of it true
VdW value. When the value of ssssoooollllvvvveeeennnntttt is ttttrrrruuuueeee,,,, 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 ssssoooollllvvvveeeennnntttt and changing ssssoooollllvvvveeeennnntttt
resets rrrraaaaddddiiiiuuuussss to its new default value.
SSSSeeeetttt SSSShhhhaaaaddddoooowwww
The RasMol sssseeeetttt sssshhhhaaaaddddoooowwww 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 com-
mand ssssllllaaaabbbb ooooffffffff.... Raytracing typically takes about 10s for
a moderately sized protein. It is recommended that
shadowing is normally disabled whilst the molecule is
being transformed or manipulated, and only enabled once
an appropiate viewpoint is selected, to provide a
greater impression of depth.
SSSSeeeetttt SSSSllllaaaabbbbMMMMooooddddeeee
The RasMol ssssllllaaaabbbbmmmmooooddddeeee parameter controls the rendering
method of objects cut by the slabbing (z-clipping)
plane. Valid slabmode parameters are "reject", "half",
"hollow", "solid" and "section".
SSSSeeeetttt SSSSoooollllvvvveeeennnntttt
The RasMol sssseeeetttt ssssoooollllvvvveeeennnntttt command is used to control the
behaviour of the RasMol ddddoooottttssss command. Depending upon
Sun Microsystems Last change: October 1994 16
RASMOL(1) User Commands RASMOL(1)
the value of the ssssoooollllvvvveeeennnntttt parameter, the ddddoooottttssss command
either generates a Van der Waal's or a solvent acessi-
ble surface around the currently selected set of atoms.
Changing this parameter automatically resets the value
of the RasMol rrrraaaaddddiiiiuuuussss parameter. The command sssseeeetttt ssssoooollll----
vvvveeeennnntttt ffffaaaallllsssseeee,,,, the default value, indicates that a Van der
Waal's surface should be generated and resets the value
of rrrraaaaddddiiiiuuuussss to zero. The command sssseeeetttt ssssoooollllvvvveeeennnntttt ttttrrrruuuueeee indi-
cates that a `Connolly' or `Richards' solvent accessi-
ble surface should be drawn and sets the rrrraaaaddddiiiiuuuussss parame-
ter, the solvent radius, to 1.2 Angstroms (or 300
RasMol units).
SSSSeeeetttt SSSSppppeeeeccccuuuullllaaaarrrr
The RasMol sssseeeetttt ssssppppeeeeccccuuuullllaaaarrrr 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.
The specular highlights on the surfaces of solid
objects may be altered by using the specular reflection
coefficient, which is altered using the RasMol sssseeeetttt
ssssppppeeeeccccppppoooowwwweeeerrrr command.
SSSSeeeetttt SSSSppppeeeeccccPPPPoooowwwweeeerrrr
The ssssppppeeeeccccppppoooowwwweeeerrrr parameter determines the shininess of
solid objects rendered by RasMol. This value between 0
and 100 adjusts the reflection coeffient used in specu-
lar highlight calculations. The specular highlights are
enabled and disabled by the RasMol sssseeeetttt ssssppppeeeeccccuuuullllaaaarrrr com-
mand. 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.
SSSSeeeetttt SSSSSSSSBBBBoooonnnnddddssss
The RasMol ssssssssbbbboooonnnnddddssss parameter determines whether disul-
phide 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 ssssssssbbbboooonnnnddddssss command. Drawing disulphide bridges between
alpha carbons is useful when the rest of the protein is
shown in only a schematic representation such as bbbbaaaacccckkkk----
bbbboooonnnneeee,,,, rrrriiiibbbbbbbboooonnnnssss or ssssttttrrrraaaannnnddddssss.... his parameter is similar to
the RasMol hhhhbbbboooonnnnddddssss parameter.
Sun Microsystems Last change: October 1994 17
RASMOL(1) User Commands RASMOL(1)
SSSSeeeetttt SSSSttttrrrraaaannnnddddssss
The RasMol ssssttttrrrraaaannnnddddssss 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 rrrriiiibbbbbbbboooonnnnssss com-
mand.
SSSSeeeetttt UUUUnnnniiiittttCCCCeeeellllllll
The RasMol uuuunnnniiiittttcccceeeellllllll 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
data file. The RasMol command sssshhhhoooowwww ssssyyyymmmmmmmmeeeettttrrrryyyy display
details of the crystal's space group and unit cell
axes. The sssseeeetttt uuuunnnniiiittttcccceeeellllllll command is similar the the com-
mands sssseeeetttt aaaaxxxxeeeessss and sssseeeetttt bbbboooouuuunnnnddddbbbbooooxxxx that display orthogonal
co-ordinate axes and the bounding box respectively.
SSSSeeeetttt VVVVeeeeccccttttPPPPSSSS
The RasMol vvvveeeeccccttttppppssss parameter is use to control the way
in which the RasMol wwwwrrrriiiitttteeee command generates vector
PostScript output files. The command sssseeeetttt vvvveeeeccccttttppppssss oooonnnn
enables to 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 by not large spacefilling
spheres models. Cartoon outlines can be disabled, the
default, by the command sssseeeetttt vvvveeeeccccttttppppssss ooooffffffff
AAAATTTTOOOOMMMM EEEEXXXXPPPPRRRREEEESSSSSSSSIIIIOOOONNNNSSSS
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, wwwwiiiitttthhhhiiiinnnn expressions, or logical (boolean) combina-
tions of the above expression types.
The logical operators allow complex queries to be con-
structed out of simpler ones using the standard boolean con-
nectives aaaannnndddd,,,, oooorrrr and nnnnooootttt.... These may be abbreviated by the
symbols "&", "|" and "!" respectively. Parentheses (brack-
ets) may be used to alter the precedence of the operators.
For convenience, a comma may also be used for boolean dis-
junction.
Sun Microsystems Last change: October 1994 18
RASMOL(1) User Commands RASMOL(1)
The atom expression is evaluated for each atom, hence pppprrrroooo----
tttteeeeiiiinnnn aaaannnndddd bbbbaaaacccckkkkbbbboooonnnneeee selects protein bacbone atoms, not the
protein and [nucleic] acid backbone atoms!
PPPPrrrriiiimmmmiiiittttiiiivvvveeee EEEExxxxpppprrrreeeessssssssiiiioooonnnnssss
RasMol primitive expressions are the fundamental build-
ing blocks of atom expressions. There are two types of
primitive expression. The first type is used to iden-
tify 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 sssseeeelllleeeecccctttt 5555,,,,6666,,,,7777,,,,8888 is also sssseeeelllleeeecccctttt 5555----8888.... Note
that this selects the given residue numbers in all
macromolecule chains.
The second type of primitive expression specifies a
sequence of fields that must match for a given atom.
The first part specifies a residue (or group of resi-
dues) and an optional second part specifies the atoms
within those residues. The first part consists of a
residue name, optionally followed by a residue number
and/or chain identifier. The second part consists of a
period character followed by an atom name. An asterisk
may be used as a wild card for a whole field and a
question mark as a single character wildcard.
CCCCoooommmmppppaaaarrrriiiissssoooonnnn OOOOppppeeeerrrraaaattttoooorrrrssss
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.
The atom properties that may be used in RasMol are
aaaattttoooommmmnnnnoooo for the atom serial number, eeeelllleeeemmmmnnnnoooo for the
atom's atomic number (element), rrrreeeessssnnnnoooo for the residue
number, rrrraaaaddddiiiiuuuussss for the spacefill radius in RasMol units
(or zero if not represented as a sphere) and tttteeeemmmmppppeeeerrrraaaa----
ttttuuuurrrreeee for the PDB anisotropic temperature value.
The equality operator is denoted either "=" or "==".
The inequality operator as either "<>", "!=" or "/=".
The ordering operators are "<" for less than, "<=" for
less than or equal to, ">" for greater than, and ">"
for greater than or equal to.
WWWWiiiitttthhhhiiiinnnn EEEExxxxpppprrrreeeessssssssiiiioooonnnnssss
A RasMol wwwwiiiitttthhhhiiiinnnn expression allows atoms to be selected
Sun Microsystems Last change: October 1994 19
RASMOL(1) User Commands RASMOL(1)
on their proximity to another set of atoms. A wwwwiiiitttthhhhiiiinnnn
expression takes two parameters separated by a comma
and surrounded by parenthesis. 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 wwwwiiiitttthhhhiiiinnnn expressions.
For example, the command sssseeeelllleeeecccctttt wwwwiiiitttthhhhiiiinnnn((((3333....2222,,,,bbbbaaaacccckkkkbbbboooonnnneeee))))
selects any atom within a 3.2 Angstrom radius of any
atom in a protein or nucleic acid backbone. WWWWiiiitttthhhhiiiinnnn
expressions are particularly useful for selecting the
atoms around an active site.
PPPPrrrreeeeddddeeeeffffiiiinnnneeeedddd SSSSeeeettttssss
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 primitive atom expressions, and in some
cases of selecting 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 sssseeeelllleeeecccctttt ooooxxxxyyyyggggeeeennnn is
equivalent to the command sssseeeelllleeeecccctttt eeeelllleeeemmmmnnnnoooo====8888....
PPPPrrrreeeeddddeeeeffffiiiinnnneeeedddd SSSSeeeettttssss
AAAATTTT SSSSeeeetttt
This set contains the atoms in the complementary
nucleotides adenosine and thymidine (A and T respec-
tively). All nucleotides are classified as either the
set aaaatttt or the set ccccgggg This set is equivalent to the
RasMol atom expressions aaaa,,,,tttt and nnnnuuuucccclllleeeeiiiicccc aaaannnndddd nnnnooootttt ccccgggg
AAAAcccciiiiddddiiiicccc SSSSeeeetttt
The set of acidic amino acids. These are the residue
types Asp and Glu. All amino acids are classified as
either aaaacccciiiiddddiiiicccc,,,, bbbbaaaassssiiiicccc oooorrrr nnnneeeeuuuuttttrrrraaaallll.... This set is equivalent
to the RasMol atom expressions aaaasssspppp,,,, gggglllluuuu and aaaammmmiiiinnnnoooo aaaannnndddd
nnnnooootttt ((((bbbbaaaassssiiiicccc oooorrrr nnnneeeeuuuuttttrrrraaaallll))))
AAAAccccyyyycccclllliiiicccc SSSSeeeetttt
The set of atoms in amino acids not containing a cycle
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RASMOL(1) User Commands RASMOL(1)
or ring. All amino acids are classified as either
ccccyyyycccclllliiiicccc or aaaaccccyyyycccclllliiiicccc.... This set is equivalent to the RasMol
atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ccccyyyycccclllliiiicccc
AAAAlllliiiipppphhhhaaaattttiiiicccc SSSSeeeetttt
This set contains the aliphatic amino acids. These are
the amino acids Ala, Gly, Ile, Leu and Val. This set
is equiavlent to the RasMol atom expression aaaallllaaaa,,,, ggggllllyyyy,,,,
iiiilllleeee,,,, lllleeeeuuuu,,,, vvvvaaaallll
AAAAllllpppphhhhaaaa SSSSeeeetttt
The set of alpha carbons in the protein molecule. This
set is approximately equivalent to the RasMol atom
expression ****....CCCCAAAA This command should not be confused
with the predefined set hhhheeeelllliiiixxxx which contains the atoms
in the amino acids of the protein's alpha helices.
AAAAmmmmiiiinnnnoooo SSSSeeeetttt
This set contains all the atoms contained in amino acid
residues. This is useful for distinguishing the pro-
tein from the nucleic acid and heterogenous atoms in
the current molecule database.
AAAArrrroooommmmaaaattttiiiicccc SSSSeeeetttt
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 ccccyyyycccclllliiiicccc....
This set is equivalent to the RasMol atom expressions
hhhhiiiissss,,,, pppphhhheeee,,,, ttttrrrrpppp,,,, ttttyyyyrrrr and ccccyyyycccclllliiiicccc aaaannnndddd nnnnooootttt pppprrrroooo
BBBBaaaacccckkkkbbbboooonnnneeee SSSSeeeetttt
This set contains the four atoms of each amino acid
that form the polypeptide N-C-C-O backbone of proteins,
and the atoms the sugar phosphate backbone of nucleic
acids. Use the RasMol predefined sets pppprrrrooootttteeeeiiiinnnn and
nnnnuuuucccclllleeeeiiiicccc to distinguish between the two forms of back-
bone. Atoms in nucleic acids and proteins are either
bbbbaaaacccckkkkbbbboooonnnneeee or ssssiiiiddddeeeecccchhhhaaaaiiiinnnn.... This set is equivalent to the
RasMol expression ((((pppprrrrooootttteeeeiiiinnnn oooorrrr nnnnuuuucccclllleeeeiiiicccc)))) aaaannnndddd nnnnooootttt
ssssiiiiddddeeeecccchhhhaaaaiiiinnnn
The predefined set mmmmaaaaiiiinnnncccchhhhaaaaiiiinnnn is synonymous with the set
bbbbaaaacccckkkkbbbboooonnnneeee....
BBBBaaaassssiiiicccc SSSSeeeetttt
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RASMOL(1) User Commands RASMOL(1)
The set of basic amino acids. These are the residue
types Arg, His and Lys. All amino acids are classified
as either aaaacccciiiiddddiiiicccc,,,, bbbbaaaassssiiiicccc or nnnneeeeuuuuttttrrrraaaallll.... This set is
equivalent to the RasMol atom expressions aaaarrrrgggg,,,, hhhhiiiissss,,,, llllyyyyssss
and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((aaaacccciiiiddddiiiicccc oooorrrr nnnneeeeuuuuttttrrrraaaallll))))
BBBBoooonnnnddddeeeedddd SSSSeeeetttt
This set contain all the atoms in the current molecule
database that are bonded to atleast one other atom.
BBBBuuuurrrriiiieeeedddd SSSSeeeetttt
This set contains the atoms in those amino acids that
tend (prefer) to buried inside protein, away from con-
tact with solvent molecules. This set refers to the
amino acids preference and not the actual solvent aces-
sibility for the current protein. All amino acids are
classified as either ssssuuuurrrrffffaaaacccceeee or bbbbuuuurrrriiiieeeedddd.... This set is
equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt
ssssuuuurrrrffffaaaacccceeee
CCCCGGGG SSSSeeeetttt
This set contains the atoms in the complementary
nucleotides cytidine and guanoine (C and G respec-
tively). All nucleotides are classified as either the
set aaaatttt or the set ccccgggg This set is equivalent to the
RasMol atom expressions cccc,,,,gggg and nnnnuuuucccclllleeeeiiiicccc aaaannnndddd nnnnooootttt aaaatttt
CCCChhhhaaaarrrrggggeeeedddd SSSSeeeetttt
This set contains the charged amino acids. These are
the amino acids that are either aaaacccciiiiddddiiiicccc or bbbbaaaassssiiiicccc.... Amino
acids are classified as being either cccchhhhaaaarrrrggggeeeedddd or nnnneeeeuuuu----
ttttrrrraaaallll.... This set is equivalent to the RasMol atom expres-
sions aaaacccciiiiddddiiiicccc oooorrrr bbbbaaaassssiiiicccc and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt nnnneeeeuuuuttttrrrraaaallll
CCCCyyyycccclllliiiicccc SSSSeeeetttt
The set of atoms in amino acids containing a cycle or
rings. All amino acids are classified as either ccccyyyycccclllliiiicccc
or aaaaccccyyyycccclllliiiicccc.... This set consists of the amino acids His,
Phe, Pro, Trp and Tyr. The members of the predefined
set aaaarrrroooommmmaaaattttiiiicccc are members of this set. The only cyclic
but non-aromatic amino acid is proline. This set is
equivalent to the RasMol atom expressions hhhhiiiissss,,,, pppphhhheeee,,,,
pppprrrroooo,,,, ttttrrrrpppp,,,, ttttyyyyrrrr and aaaarrrroooommmmaaaattttiiiicccc oooorrrr pppprrrroooo and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt
aaaaccccyyyycccclllliiiicccc
CCCCyyyyssssttttiiiinnnneeee SSSSeeeetttt
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RASMOL(1) User Commands RASMOL(1)
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 ccccyyyyssssttttiiiinnnneeee nor the RasMol
ssssssssbbbboooonnnnddddssss command have been used since the molecule was
loaded. The set of free cysteines may be determined
using the RasMol atom expression ccccyyyyssss aaaannnndddd nnnnooootttt ccccyyyyssssttttiiiinnnneeee
HHHHeeeelllliiiixxxx SSSSeeeetttt
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 ssssttttrrrruuuuccccttttuuuurrrreeee command.
This predefined set should not be confused with the
predefined set aaaallllpppphhhhaaaa which contains the alpha carbon
atoms of a protein.
HHHHeeeetttteeeerrrroooo SSSSeeeetttt
This set contains all the heterogenous 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 hhhheeeetttteeeerrrroooo
atoms are classified as either lllliiiiggggaaaannnndddd or ssssoooollllvvvveeeennnntttt atoms.
These heterogenous ssssoooollllvvvveeeennnntttt atoms are further classified
as either wwwwaaaatttteeeerrrr or iiiioooonnnnssss....
HHHHyyyyddddrrrrooooggggeeeennnn SSSSeeeetttt
This predefined set contains all the hydrogen and deu-
terium atoms of the current molecule. This predefined
set is equivalent to the RasMol atom expression
eeeelllleeeemmmmnnnnoooo====1111
HHHHyyyyddddrrrroooopppphhhhoooobbbbiiiicccc SSSSeeeetttt
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
hhhhyyyyddddrrrroooopppphhhhoooobbbbiiiicccc or ppppoooollllaaaarrrr.... This set is equivalent to the
RasMol atom expressions aaaallllaaaa,,,, lllleeeeuuuu,,,, vvvvaaaallll,,,, iiiilllleeee,,,, pppprrrroooo,,,, pppphhhheeee,,,,
and aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ppppoooollllaaaarrrr
IIIIoooonnnnssss SSSSeeeetttt
This set contains all the heterogenous phosphate and
sulphate ions in the current molecule data file. A
large number of these ions are sometimes associated
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RASMOL(1) User Commands RASMOL(1)
with protein and nucleic acid structures determined by
X-ray crystallography. These atoms tend to clutter an
image. All hhhheeeetttteeeerrrroooo atoms are classified as either lllliiiiggggaaaannnndddd
or ssssoooollllvvvveeeennnntttt atoms. All ssssoooollllvvvveeeennnntttt atoms are classified as
either wwwwaaaatttteeeerrrr or iiiioooonnnnssss....
LLLLaaaarrrrggggeeee SSSSeeeetttt
All amino acids are classified as either ssssmmmmaaaallllllll,,,, mmmmeeeeddddiiiiuuuummmm
or llllaaaarrrrggggeeee.... This set is equivalent to the RasMol atom
expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((ssssmmmmaaaallllllll oooorrrr mmmmeeeeddddiiiiuuuummmm))))
LLLLiiiiggggaaaannnndddd SSSSeeeetttt
This set contains all the heterogenous cofactor and
ligand moieties that are contained in the current
molecule data file. At this set is defined to be all
hhhheeeetttteeeerrrroooo atoms that are not ssssoooollllvvvveeeennnntttt atoms. Hence this set
is equivalent to the RasMol atom expression hhhheeeetttteeeerrrroooo aaaannnndddd
nnnnooootttt ssssoooollllvvvveeeennnntttt
MMMMeeeeddddiiiiuuuummmm SSSSeeeetttt
All amino acids are classified as either ssssmmmmaaaallllllll,,,, mmmmeeeeddddiiiiuuuummmm
or llllaaaarrrrggggeeee.... This set is equivalent to the RasMol atom
expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((llllaaaarrrrggggeeee oooorrrr ssssmmmmaaaallllllll))))
NNNNeeeeuuuuttttrrrraaaallll SSSSeeeetttt
The set of neutral amino acids. All amino acids are
classified as either aaaacccciiiiddddiiiicccc,,,, bbbbaaaassssiiiicccc or nnnneeeeuuuuttttrrrraaaallll.... This set
is equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd
nnnnooootttt ((((aaaacccciiiiddddiiiicccc oooorrrr bbbbaaaassssiiiicccc))))
NNNNuuuucccclllleeeeiiiicccc SSSSeeeetttt
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 ppppuuuurrrriiiinnnneeee or
ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeee.... This set is equivalent to the RasMol atom
expressions aaaa,,,,cccc,,,,gggg,,,,tttt and ppppuuuurrrriiiinnnneeee oooorrrr ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeee
PPPPoooollllaaaarrrr SSSSeeeetttt
This set contains the polar amino acids. All amino
acids are classified as either hhhhyyyyddddrrrroooopppphhhhoooobbbbiiiicccc or ppppoooollllaaaarrrr....
This set is equivalent to the RasMol atom expression
aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt hhhhyyyyddddrrrroooopppphhhhoooobbbbiiiicccc
PPPPrrrrooootttteeeeiiiinnnn SSSSeeeetttt
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RASMOL(1) User Commands RASMOL(1)
The set of all atoms in proteins. This consists of the
RasMol predefined set aaaammmmiiiinnnnoooo and common post-translation
modifications.
PPPPuuuurrrriiiinnnneeee SSSSeeeetttt
The set of purine nucleotides. These are the bases
adenosine and guanosine (A and G respectively). All
nucleotides are either ppppuuuurrrriiiinnnneeeessss or ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeeessss.... This set
is equivalent to the RasMol atom expressions aaaa,,,,gggg and
nnnnuuuucccclllleeeeiiiicccc aaaannnndddd nnnnooootttt ppppuuuurrrriiiinnnneeee
PPPPyyyyrrrriiiimmmmiiiiddddiiiinnnneeee SSSSeeeetttt
The set of pyrimidine nucleotides. These are the bases
cytidine and thymidine (C and T respectively). All
nucleotides are either ppppuuuurrrriiiinnnneeeessss or ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeeessss.... This set
is equivalent to the RasMol atom expressions cccc,,,,tttt and
nnnnuuuucccclllleeeeiiiicccc aaaannnndddd nnnnooootttt ppppyyyyrrrriiiimmmmiiiiddddiiiinnnneeee
SSSSeeeelllleeeecccctttteeeedddd SSSSeeeetttt
This set contains the set of atoms in the currently
selected region. The currently selected region is
defined by the preceding sssseeeelllleeeecccctttt or rrrreeeessssttttrrrriiiicccctttt command and
not the atom expression containing the sssseeeelllleeeecccctttteeeedddd key-
word.
SSSShhhheeeeeeeetttt SSSSeeeetttt
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 ssssttttrrrruuuuccccttttuuuurrrreeee command.
SSSSiiiiddddeeeecccchhhhaaaaiiiinnnn SSSSeeeetttt
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 pppprrrrooootttteeeeiiiinnnn and
nnnnuuuucccclllleeeeiiiicccc to distinguish between the two forms of
sidechain. Atoms in nucleic acids and proteins are
either bbbbaaaacccckkkkbbbboooonnnneeee or ssssiiiiddddeeeecccchhhhaaaaiiiinnnn.... This set is equivalent to
the RasMol expression ((((pppprrrrooootttteeeeiiiinnnn oooorrrr nnnnuuuucccclllleeeeiiiicccc)))) aaaannnndddd nnnnooootttt
bbbbaaaacccckkkkbbbboooonnnneeee
SSSSmmmmaaaallllllll SSSSeeeetttt
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RASMOL(1) User Commands RASMOL(1)
All amino acids are classified as either ssssmmmmaaaallllllll,,,, mmmmeeeeddddiiiiuuuummmm
or llllaaaarrrrggggeeee.... This set is equivalent to the RasMol atom
expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt ((((mmmmeeeeddddiiiiuuuummmm oooorrrr llllaaaarrrrggggeeee))))
SSSSoooollllvvvveeeennnntttt SSSSeeeetttt
This set contains the solvent atoms in the molecule
co-ordinate file. These are the heterogenous water
molecules, phosphate and sulphate ions. All hhhheeeetttteeeerrrroooo
atoms are classified as either lllliiiiggggaaaannnndddd or ssssoooollllvvvveeeennnntttt atoms.
All ssssoooollllvvvveeeennnntttt atoms are classified as either wwwwaaaatttteeeerrrr or
iiiioooonnnnssss.... This set is equivalent to the RasMol atom expres-
sions hhhheeeetttteeeerrrroooo aaaannnndddd nnnnooootttt lllliiiiggggaaaannnndddd and wwwwaaaatttteeeerrrr oooorrrr iiiioooonnnnssss
SSSSuuuurrrrffffaaaacccceeee SSSSeeeetttt
This set contains the atoms in those amino acids that
tend (prefer) to be on the surface of proteins, in con-
tact 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 ssssuuuurrrrffffaaaacccceeee or bbbbuuuurrrriiiieeeedddd.... This set is
equivalent to the RasMol atom expression aaaammmmiiiinnnnoooo aaaannnndddd nnnnooootttt
bbbbuuuurrrriiiieeeedddd
TTTTuuuurrrrnnnn SSSSeeeetttt
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 ssssttttrrrruuuuccccttttuuuurrrreeee command.
WWWWaaaatttteeeerrrr SSSSeeeetttt
This set contains all the heterogenous 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 crystallog-
raphy. These atoms tend to clutter an image. All
hhhheeeetttteeeerrrroooo atoms are classified as either lllliiiiggggaaaannnndddd or ssssoooollllvvvveeeennnntttt
atoms. The ssssoooollllvvvveeeennnntttt atoms are further classified as
either wwwwaaaatttteeeerrrr or iiiioooonnnnssss....
CCCCOOOOLLLLOOOOUUUURRRR SSSSCCCCHHHHEEEEMMMMEEEESSSS
The RasMol ccccoooolllloooouuuurrrr 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 sup-
ports ccccppppkkkk,,,, aaaammmmiiiinnnnoooo,,,, cccchhhhaaaaiiiinnnn,,,, ggggrrrroooouuuupppp,,,, sssshhhhaaaappppeeeellllyyyy,,,, ssssttttrrrruuuuccccttttuuuurrrreeee,,,,
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RASMOL(1) User Commands RASMOL(1)
tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee,,,, cccchhhhaaaarrrrggggeeee and uuuusssseeeerrrr colour schemes for atoms, a
hhhhbbbboooonnnndddd ttttyyyyppppeeee colour scheme for hydrogen bonds and eeeelllleeeeccccttttrrrroooossss----
ttttaaaattttiiiicccc ppppooootttteeeennnnttttiiiiaaaallll colour scheme for dot surfaces. The
currently predefined colour names are blue, black, cyan,
green, greenblue, magenta, orange, purple, red, redorange,
violet, white and yellow.
AAAAmmmmiiiinnnnoooo CCCCoooolllloooouuuurrrrssss
The RasMol aaaammmmiiiinnnnoooo 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 sssshhhhaaaappppeeeellllyyyy
scheme.
CCCChhhhaaaaiiiinnnn CCCCoooolllloooouuuurrrrssss
The RasMol cccchhhhaaaaiiiinnnn colour scheme assigns each macromolec-
ular chain a unique colour. This colour scheme is par-
ticularly useful for distinguishing the parts of mul-
timeric structure or the individual `strands' of a DNA
chain.
CCCCPPPPKKKK CCCCoooolllloooouuuurrrrssss
The RasMol ccccppppkkkk colour scheme is based upon the colours
of the popular plastic spacefilling models which were
developed by Corey, Pauling and later improved by Kul-
tun. This colour scheme colour `atom' objects by the
atom (element) type. This is the scheme conventionally
used by chemists.
GGGGrrrroooouuuupppp CCCCoooolllloooouuuurrrrssss
The RasMol ggggrrrroooouuuupppp 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 pro-
teins 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 heterogenous molecules associated with it,
the macromolecule may not be drawn in the full `range'
of the spectrum.
SSSShhhhaaaappppeeeellllyyyy CCCCoooolllloooouuuurrrrssss
The RasMol sssshhhhaaaappppeeeellllyyyy colour scheme colour codes residues
by amino acid property. This scheme is based upon Bob
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RASMOL(1) User Commands RASMOL(1)
Fletterick's "Shapely Models". Each amino acid and
nucleic acid residue is given a unique colour. The
sssshhhhaaaappppeeeellllyyyy colour scheme is used by David Bacon's Raster3D
program. This colour scheme is similar to the aaaammmmiiiinnnnoooo
colour scheme.
SSSSttttrrrruuuuccccttttuuuurrrreeee CCCCoooolllloooouuuurrrrssss
The RasMol ssssttttrrrruuuuccccttttuuuurrrreeee 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 and SHEET records), if available, or deter-
mined using Kabsch and Sander's DSSP algorithm. The
RasMol ssssttttrrrruuuuccccttttuuuurrrreeee command may be used to force DSSP's
structure assignment to be used.
TTTTeeeemmmmppppeeeerrrraaaattttuuuurrrreeee CCCCoooolllloooouuuurrrrssss
The RasMol tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee 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.
The difference between the tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee and cccchhhhaaaarrrrggggeeee
colour schemes is that increasing temperature values
proceed from blue to red, whereas increasing charge
valuse go from red to blue.
CCCChhhhaaaarrrrggggeeee CCCCoooolllloooouuuurrrrssss
The RasMol cccchhhhaaaarrrrggggeeee 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.
The difference between the cccchhhhaaaarrrrggggeeee and tttteeeemmmmppppeeeerrrraaaattttuuuurrrreeee
colour schemes is that increasing temperature values
proceed from blue to red, whereas increasing charge
Sun Microsystems Last change: October 1994 28
RASMOL(1) User Commands RASMOL(1)
valuse go from red to blue.
If the charge/temperature field stores reasonable
values it is possible to use the RasMol ccccoooolllloooouuuurrrr ddddoooottttssss
ppppooootttteeeennnnttttiiiiaaaallll command to colour code a dot surface (gen-
erated by the ddddoooottttssss command) by electrostatic potential.
UUUUsssseeeerrrr CCCCoooolllloooouuuurrrrssss
The RasMol uuuusssseeeerrrr 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.
HHHHBBBBoooonnnndddd TTTTyyyyppppeeee CCCCoooolllloooouuuurrrrssss
The RasMol ttttyyyyppppeeee colour scheme applies only to hydrogen
bonds, hence is used in the command ccccoooolllloooouuuurrrr hhhhbbbboooonnnnddddssss ttttyyyyppppeeee
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).
PPPPooootttteeeennnnttttiiiiaaaallll CCCCoooolllloooouuuurrrrssss
The RasMol ppppooootttteeeennnnttttiiiiaaaallll colour scheme applies only to dot
surfaces, hence is used in the command ccccoooolllloooouuuurrrr ddddoooottttssss
ppppooootttteeeennnnttttiiiiaaaallll 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 ccccoooolllloooouuuurrrr cccchhhhaaaarrrrggggeeee command.
Like the cccchhhhaaaarrrrggggeeee colour scheme low values are blue/white
and high values are red.
SSSSEEEEEEEE AAAALLLLSSSSOOOO
The RasMol User Manual!
AAAAUUUUTTTTHHHHOOOORRRR
Copyright (C) 1992-94 by Roger Sayle. All rights reserved.
(rasmol@ggr.co.uk)
Sun Microsystems Last change: October 1994 29
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