Back to the OMM Exhibits
An Introduction to
Chime Scripting
Nathan Silva and David Marcey
CLU Biology Department
©David Marcey, 2001
I. Introduction
II. Display
III. Loading and Positioning
IV. The Select Command and Labeling
V. Coloring and Schemes
VI. Illustrating Bonds
VII. Animation
Note: 1) This exhibit is best viewed if the cue buttons ( ) are pressed in
sequence and if the viewer does not independently manipulate the molecule on
the left; 2) The Chime scripts in this exhibit are samples; the reader is
encouraged to study the Chime/RasMol manual for a comprehensive list of
scripting commands.
I. Introduction
Chime, a browser plugin used to view molecules in web pages, can read scripts that are
contained in embedded buttons. These scripts are used to change the rendering of the molecule
to illustrate important structural features.
This exhibit provides example Chime scripts that can be copied and pasted into the embed tags
for buttons. Each section starts with a discussion of the uses of various renderings and ends with
a table that includes an extensive list of buttons (left column) containing sample scripts (right
column). These evoke particular renderings of the molecules displayed in the left frame. If you are
new to Chime scripting, it is suggested that you spend time going through the exhibit in its
entirety, reading the scripts to see how they can be employed in your own web pages.
II. Display
Chime uses two different units of measurement that can be used with display commands. One is
the standard, atomic-resolution unit, the Angstrom (Å); 1 Å = 10-10 meters. Chime also uses a
novel unit, the RasMol unit; 1 RasMol unit = 1/250 Å. The display codes (see below) can be
modified to specify dimensions in either RasMol units or Angstroms by adding a numerical value
after the name of a command. Angstroms are indicated by a decimal in the numerical value and
RasMol units are used as a default when no decimals are employed. For example, a "wireframe
125" script specifies a wireframe display in 125 RasMol Units. This is equivalent to the script
"wireframe 0.5" (0.5 Å).
The default display for most pdbs is wireframe, as shown at left. Wireframe is very useful
because it clearly shows the covalent bonds (except S-S bonds) between all atoms of a molecule.
Varying the thickness of wireframe displays can provide useful alternatives in illustrating points.
Wireframe can also be displayed as a dashed line instead of a solid line (see below).
Spacefill is another commonly used display. Spacefill rendering displays the Van der Waals
radius of each atom as a solid sphere by default.
Spacefill radii can be altered by a numerical specification (see below).
Dots is a display similar to spacefill in that the diameter of the spheres formed are equal to that of
the Van der Waals radius. The density of dots can be modified by numerical specifications (see
below). Dots combines easily with other display commands to provide useful effects. Combining
wireframe and dots displays can show Van der Waals surfaces clearly for a loop or secondary
structure.
So far, we have considered displays that affect all atoms of a molecule, unless particular atoms
are selected (see below, The Select Command). Sometimes showing only the backbone of a
molecule is desired. There are several displays that illustrate the backbone conformation of a
molecule:
The backbone display shows the polypeptide backbone of a protein or the sugarphosphate backbone of a nucleic acid as a train of bonds connecting the
adjacent alpha carbons of each amino acid in sequential order. Backbones can
be displayed in a dashed line (see below).
Trace is a display similar to backbone, but with smoothed transitions between the
amino acids of a peptide chain or nucleotides of nucleic acids.
There are two displays that are excellent for showing secondary structure:
ribbons; cartoons. Both smooth the backbone, like trace, but display the
backbone as a wide, flattened ribbon. Numerical modifications can be used to
change the width of the backbone. In default mode, the width of alpha helical and
beta strand secondary structure is greater than that of loops. Cartoon has the
feature of indicating amino-carboxy polarity. This is quite convenient, e.g. when
showing the parallel or antiparallel arrangement of b strands.
Strands is a rendering similar to ribbons and cartoons, but with the backbones
displayed as a series of thin lines. Strands can be indicated with dashed lines
(see below).
Surface rendering is very useful in showing binding pockets and/or non-covalent interactions, but
surface calculations take significant amounts of time. Surface commands should therefore be
used judiciously in molecular exhibits.
Lighting effects can be employed to change the appearance of a molecular display.
Ambient lighting intensity can be manipulated.
Specular highlights on atoms are white reflections of the "light source". The degree of specular
highlighting can be changed.
Please turn molecule display off before proceeding with the table buttons below.
Display Commands
Buttons/Effects
code for button = <embed type = "application/xspt" width=15 height=15 button=followed
target="molecule" script="Chime Scripts
Here"></embed>
Chime Scripts in buttons
Cut and paste in " " in button code
wireframe (default = 1 RasMol unit)
select all; wireframe;
wireframe 10 (10 RasMol units = 0.04 Å)
wireframe 10;
wireframe 50 (50 RasMol units = 0.2 Å)
wireframe 50;
wireframe 100 (100 RasMol units = 0.4 Å)
wireframe 100;
wireframe 0.5 (0.5 Å = 125 RasMol units)
wireframe 0.5;
dashed wireframe
wireframe dash;
spacefill (default = Van der Waals radius)
wireframe off; spacefill;
spacefill 50 (50 RasMol units = 0.2 Å)
spacefill 50;
spacefill 100 (100 RasMol units = 0.4 Å)
spacefill 100;
spacefill 500 (500 RasMol units =2.0 Å)
spacefill 500;
spacefill 0.5 (0.5 Å = 125 RasMol units)
spacefill 0.5;
dots (default = ~100 dots per medium sized atom)
spacefill off; dots;
dots 10 (~10 dots per medium sized atom)
dots 10;
dots 100 (~100 dots per medium sized atom)
dots100;
dots 250 (~250 dots per medium sized atom)
dots 250;
dots wireframe combo
wireframe 100; dots
backbone (default = 1 RasMol unit)
dots off; wireframe off; backbone;
backbone 10 (10 RasMol units = 0.04 Å)
backbone 10;
backbone 50 (50 RasMol units = 0.2 Å)
backbone 50;
backbone 100 (100 RasMol units = 0.4 Å)
backbone 100;
backbone 0.5 (0.5 Å = 125 RasMol units)
backbone 0.5;
dashed backbone
backbone dash;
trace (default = 90 RasMol units)
backbone off; trace;
trace 10 (10 RasMol units = 0.04 Å)
trace 10;
trace 50 (50 RasMol units = 0.2 Å)
trace 50;
trace 100 (100 RasMol units = 0.4 Å)
trace 100;
trace 0.5 (0.5 Å = 125 RasMol units)
trace 0.5;
ribbon [default = 720 RasMol units (2.88 Å) for
nucleic acids, 380 (1.52 Å) for protein secondary
structure, and 100 (0.4 Å) for turns and random
coil]
trace off; ribbon;
ribbon 10 (10 RasMol units = 0.04 Å)
ribbon 10;
ribbon 100 (100 RasMol units = 0.4Å)
ribbon 100;
ribbon 500 (500 RasMol units =2.0 Å)
ribbon 500;
ribbon 0.5 (0.5 Å = 125 RasMol units)
ribbon 0.5;
cartoon [default = 720 RasMol units (2.88 Å) for
nucleic acids, 380 (1.52 Å) for protein secondary
structure, and 100 (0.4 Å) for turns and random
coil. Arrow heads are displayed on the C-terminus
of helices and strands and the 3' end of nucleic
acid backbones.]
ribbon off; cartoon;
cartoon 10 (10 RasMol units = 0.04 Å)
cartoon 10;
cartoon 100 (100 RasMol units = 0.4 Å)
cartoon 100;
cartoon 500 (500 RasMol units =2.0 Å)
cartoon 500;
cartoon 0.5 (0.5 Å = 125 RasMol units)
cartoon 0.5;
strands [default = 720 RasMol units (2.88 Å) for
nucleic acids, 380 (1.52 Å) for protein secondary
structure, and 100 (0.4 Å) for turns and random
coil. Default # of strands = 4]
cartoon off; strands;
strands 10 (10 RasMol units = 0.04 Å)
strands 10;
strands 100 (50 RasMol units = 0.2 Å)
strands 100;
strands 500 (100 RasMol units = 0.4 Å)
strands 500;
strands 0.5 (0.5 Å = 125 RasMol units)
strands 0.5;
3 strands
strands; set strands 3;
5 strands
strands; set strands 5;
dashed strands
strands dash;
ball and stick (standard)
strands off; wireframe 0.15; spacefill
0.45;
ball and stick small
strands off; wireframe; spacefill 50;
ball and stick medium
wireframe 25; spacefill 75;
ball and stick large
wireframe 50; spacefill 100;
create a surface, color it white
wireframe off; spacefill off; surface
molsurface white;
create a surface, color it purple
wireframe off; spacefill off; surface
molsurface purple;
make surface transparent (toggle)
wireframe 100; spacefill off; list
molsurface transparent;
molecular lipophilicity surface potential
wireframe off; spacefill off; surface
testSurf MLP;
electrostatic surface potential
surface testSurf MEP;
Back to default spacefill
list testsurf off; list molsurface off;
reset;spacefill; color cpk;
Decrease ambient lighting intensity
select all; spacefill; set ambient 5;
Increase ambient lighting intensity
select all; spacefill; set ambient 80;
"Normal" ambient lighting intensity
select all; spacefill; set ambient 40;
Turn on specular highlights; set low specular
highlight intensity
select all; spacefill; set specular on; set
specpower 5;
set higher specular highlight intensity
select all; spacefill; set specular on; set
specpower 100;
set "normal" specular highlight intensity
select all; spacefill; set specular on; set
specpower 20;
[I. Introduction] [II. Display] [III. Loading and Positioning]
[IV. The Select Command and Labeling] [V. Coloring and Schemes]
[VI. Illustrating Bonds] [VII. Animation]
III. Loading and Positioning
Often, one needs to discuss more than one molecule (pdb file) in a molecular exhibit.
Loading a new pdb by use of a button is a simple way to do this.
Once the new pdb is loaded it is often useful to orient the molecule in 3-D by rotating it around the
X,Y, or Z axes. Rotation commands are expressed in degrees so a rotation of 360 around a
particular axis will show no change in the orientation of the molecule.
A molecule can also be translated along the X or Y axes.
Translation along the X axis causes the molecule to move left or right.
Translation along the Y axis causes the molecule to move up or down. Note: contrary to intuition,
positive numbers for Y translation move molecules down and negative numbers move molecules
up.
Translation on the Z axis is called zoom, because it brings the molecule closer to or farther away
from the viewer. The zoom command is expressed in percentage. Thus, to double the zoom
factor, a numerical value of 200 is used.
Rotation, translation, and zoom commands to effect a desired view can be incorporated in the
initial script that embeds a pdb in an html file or in a later script that loads a new pdb.
There are other ways to move, rotate, and zoom molecules that will be discussed later, in the
Animation section.
Once a particular orientation is effected, it may be useful to restore that orientation at a later point
in an exhibit. The "view" command is an easy way to achieve this. Save the view as a number
between 0-15. Restore that specific view number to return the molecule back to that desired
position. The view restore function only affects the positioning and orientation of the molecule; it
does not recall any color or display options.
Loading and Positioning Commands
Buttons/Effects
code for button = <embed type = "application/x-spt"
width=15 height=15 button=followed
target="molecule" script="Chime Scripts
Here"></embed>
Chime Scripts in buttons
Cut and paste in " " in button code
load pdb into molecule window
zap; load 'path to the pdb file', e.g.
../pdbs/ahelix.pdb
rotate 90° on X axis
rotate x 90;
rotate -90° on X axis
rotate x -90;
rotate 90° on Y axis
rotate y 90;
rotate -90° on Y axis
rotate y -90;
rotate 90° on Z axis
rotate z 90;
rotate -90° on Z axis
rotate z -90;
translate to 10 on X axis
translate x 10;
translate to -10 on X axis
translate x -10;
translate back to 0 (center) on X axis
translate x 0;
translate 10 on Y axis
translate y 10;
translate -10 on Y axis
translate y -10;
translate back to 0 (center) on Y axis
translate y 0;
zoom to 150%
zoom 150;
zoom out to 50%
zoom 50;
restore original zoom
zoom 100;
save view "0", rotate to new orientation, save view
"1", rotate to new orientation, save view "2"
view save 0; rotate x 45; rotate y 45;
view save 1; rotate y -100; rotate x 100; view save 2
restore saved view "0"
view restore 0;
restore saved view "1"
view restore 1;
restore saved view "2"
view restore 2;
[I. Introduction] [II. Display] [III. Loading and Positioning]
[IV. The Select Command and Labeling] [V. Coloring and Schemes]
[VI. Illustrating Bonds] [VII. Animation]
IV. The Select Command and Labeling
For the display commands already discussed, and for coloring and bond options to be addressed
below, it is often desirable to limit rendering changes to particular atoms or sets of atoms. The
select command is used to specify what atoms of a pdb file will be affected by subsequent
rendering commands. There are a number of predefined sets of atoms such as "all", "backbone",
"protein", "ligand", "hetero", "helix", "sheet", etc.. "Select all" selects all atoms. "Select protein" or
"select amino" both select all of the amino acids in the pdb. "Select nucleic" selects all nucleic
acid atoms, but "select dna" or "select rna" works on specified nucleic acid residues (DNA=a,t,g,c;
RNA=a,u,g,c). "Select hetero" will select all heterogeneous atoms, including water, ions, and
ligands. "Select water" will select only the water molecules, and "select ligand" will only select the
ligand. The select command can also be used to select a specific chain in a pdb file, a single
amino acid, or even a single atom (useful!).
In selecting atoms or residues, it is possible to discriminate between chains in a pdb file that
contains multiple molecules. For example, let's say that you wish to select a single residue (#10)
on one chain of a pdb file with a dimeric protein bound to DNA (four chains). Each chain will likely
have a residue # 10. If the command "select 10" were used, four residues would be selected, one
on each of the protein chains and one on each strand of DNA. Instead, if the desired residue
(#10) is on chain A, then the script "select :a and 10" would select only residue #10 on chain A,
ignoring the residue #10s on other chains.
Define is a command that is very useful when dealing with a group of atoms that do not belong to
a predefined set, such as a phosphate on a ligand or the tail of an ATP molecule. The atoms of
interest can be associated under one group name that can then be selected with ease. The
format of the script for defining a group of atoms is "define 'name of group' 'atoms to be grouped'
".
Another type of selection is the restrict command. "Restrict" limits the display to those atoms
specified in the restrict script.
Selected atoms can be labeled using the label command. Labels can be colored, and the fontsize
height set (in pixels) using appropriate commands. The default label color is the selected atom's
color and the default fontsize is 8 pixels.
Please load the tRNA synthase/tRNA molecule before proceeding with the table buttons below.
Select and Label Commands
Buttons/Effects
code for button = <embed type = "application/x-spt"
width=15 height=15 button=followed
target="molecule" script="Chime Scripts
Here"></embed>
Chime Scripts in buttons
Cut and paste in " " in button code
select all, spacefill
select all; spacefill;
select amino, spacefill
select all; spacefill off; select amino;
spacefill;
select protein, spacefill
select all; spacefill off; select protein;
spacefill;
select nucleic, spacefill
select all; spacefill off; select nucleic;
spacefill;
select dna (i.e. a,t,g,c), spacefill
select all; spacefill off; select dna;
spacefill;
select rna (i.e. a,u,g,c), spacefill
select all; spacefill off; select rna;
spacefill;
select hetero (includes water, ions, and ligands),
spacefill
select all; spacefill off; select hetero;
spacefill;
select water, spacefill
select all; spacefill off; select water;
spacefill;
select ligand, spacefill
select all; spacefill off; select ligand;
spacefill;
select chain A, spacefill
select all; spacefill off; select :A;
spacefill;
select residue # 10, spacefill
select all; spacefill off; select 10;
spacefill;
select atom # 500, spacefill
select all; spacefill off; select atomno=
500; spacefill;
select residue # 10 on chain A, spacefill
select all; spacefill off; select :A and
10; spacefill;
define atoms 500, 501, 502 and 503 as "part"
define part atomno=500, atomno=501,
atomno=502, atomno=503;
select "part", spacefill
select all; spacefill off; select part;
spacefill;
define amino acids residues 10, 11 and 12 of chain A
as "piece"
define piece :A and 10, :A and 11, :A
and 12;
select "piece", spacefill
select all; spacefill off; select piece;
spacefill;
restrict protein
select all; spacefill off; restrict protein;
restrict nucleic
select all; wireframe; restrict nucleic;
restrict ligand
select all; wireframe; restrict ligand;
label atom number 4174 "oxygen"
select all; spacefill off; wireframe;
select atomno=4174; label oxygen;
label atom number 4174 "protein"
select all; spacefill off; wireframe;
select atomno=4174; label protein;
label atom number 4174 "4174", color label magenta,
set fontsize to 15 pixels
select all; spacefill off; wireframe;
set fontsize 25; select atomno=4174;
label atom 4174; color label magenta;
turn labels off
select all; label off;
[I. Introduction] [II. Display] [III. Loading and Positioning]
[IV. The Select Command and Labeling] [V. Coloring and Schemes]
[VI. Illustrating Bonds] [VII. Animation]
V. Coloring and Schemes
Coloring atoms, sets of atoms, or other selections is quite useful in crafting quality molecular
exhibits. Explanatory text can be co-colored with specified structural features. Chime is quite
versatile in recognizing the names of prespecified colors, HTML binhex color codes, and RGB
triplet codes.
Chime "knows" the following list of specified colors: blue, yellow, cyan, green, greenblue,
magenta, orange, purple, red, redorange, violet, white, and black.
HTML binhex and RGB triplet codes are similar in that the colors are made up of alphanumerical
values for red green and blue. For binhex, the highest value is FF and the lowest is 00 (zeros, not
O's). For RGB, the highest value is 255 and the lowest is 0. The format for binhex in Chime is
[X(Red)(Green)(Blue)], e.g. "color [XFF0088]". The format for RGB triplet codes in chime is
[(Red),(Green),(Blue)], e.g. "color [255,0,255]".
Thus far, the molecules have been shown in CPK (Corey, Pauling, Kultun) colors. "CPK" is the
default coloring scheme of Chime - it is based on atom identity. Carbon is colored light gray,
oxygen red, hydrogen white, nitrogen light blue, sulfur yellow, phosphorous orange, chlorine
green, zinc brown, sodium blue, iron purple, calcium or metals dark gray, and unknown deep
pink. In addition to CPK, Chime has access to some additional predefined color schemes (not all
schemes are discussed here):
"Amino" is a scheme that assigns colors to amino acids based on their chemical
properties, e.g. acidic, basic, hydrophobic, or polar. The colors are ASP, GLU,
CYS, MET, LYS, ARG, SER, THR, PHE, TYR, ASN, GLN, GLY, LEU, VAL, ILE,
ALA, TRP, HIS and PRO.
"Chain" is a scheme that colors each different chain in a multiple molecule pdb
file a different color.
"Group" is a scheme that colors protein chains differentially in the amino-carboxy
direction.
"Temperature" is a scheme that colors atoms according to their anisotropic
temperatures, as stored as a beta value in a pdb file. Anisotropic temperature is
indicative of of an atom's mobility or uncertainty of position. The more mobile,
"warmer" segments are colored red, progressing to more immobile blue
fragments.
"Structure" is a very useful color scheme in that it differentially colors a protein's
secondary structure ( helices and  sheets). It is best to use a display command
that illustrates secondary structure when using the structure color scheme (e.g.
ribbons, cartoon, backbone, trace, or strands - see Display section).
It is quite effective to use consistent color schemes to show some molecular features. DRuMS is
a set of seven color schemes that provides a uniform standard for coloration in molecular
exhibits. The colors used in the basic DRuMS scheme are: protein, DNA, RNA,  helix and 
sheet. For amino acids the DRuMS colors are: hydrophobic amino acids, polar acidic amino
acids, polar basic amino acids, and polar uncharged amino acids. See the DRuMS website for
further information:
It is sometimes necessary to go beyond the DRuMS schemes to illustrate important structural
features. For example, it may be useful to distinguish between several pairs of chemically similar
amino acids engaged in ionic bonding. In this case, custom colors must be used to indicate
molecular identity. Fortunately, it is easy to instruct Chime to read any user-specified color code.
Please reload the tRNA synthase/tRNA molecule before before proceeding with the table buttons
below.
Coloring Commands
Buttons/Effects
code for button = <embed type = "application/x-spt"
width=15 height=15 button=followed
target="molecule" script="Chime Scripts
Here"></embed>
Chime Scripts in buttons
Cut and paste in " " in button code
color red with name
select all; color red;
color green with HTML binhex
color [X00FF00];
color blue with RGB triplet
color [0,0,255];
thick wireframe, color cpk
select amino, nucleic; wireframe 100;
color cpk;
color amino
color amino;
color chain
color chain;
color group
color group;
color temperature
color temperature;
color structure
select all; cartoon; wireframe off;
color structure;
color DRuMS
select all; wireframe off; cartoon off;
select protein; cartoon; select rna and
backbone; trace 100; select rna and
backbone; color [Xfd0162]; select
protein and not helix; color
[X787878]; select protein and not
sheet; color [X787878]; select protein
and helix; color [Xff0080]; select
sheet; color [Xffc800];
highlight C44 of RNA in magenta
select protein and nucleic; cartoons
off; wireframe; color cpk; select 44:b;
wireframe 100;
color magenta;
select protein and nucleic; cartoons
off; wireframe; color cpk; select 44:b;
wireframe 100;
color [X66CCFF];
highlight C44 of RNA in [66CCFF]
[I. Introduction] [II. Display] [III. Loading and Positioning]
[IV. The Select Command and Labeling] [V. Coloring and Schemes]
[VI. Illustrating Bonds] [VII. Animation]
VI. Illustrating Bonds
Chime recognizes by default the standard covalent bonds linking atoms in a molecule. Disulfide
(S-S) bonds can also be displayed in Chime by the use of the "ssbonds" command. The color of
the bond is that of the two linked atoms, but it can be changed with the "color ssbonds"
command. Similarly, "hbonds" and "color hbonds" tells Chime to show and color hydrogen bonds
that are specified in the pdb file.
You may wish to illustrate a connection or bond that is not specified in a pdb file. Such arbitrary
bonds can be indicated using the "monitor" command. "Monitor" forms a dashed line between any
two specified atoms and indicates the distance (in Å) between them. The distance display can be
removed by "set monitor off".
Bond Commands
Buttons/Effects
code for button = <embed type = "application/x-spt"
width=15 height=15 button=followed
target="molecule" script="Chime Scripts
Here"></embed>
Chime Scripts in buttons
Cut and paste in " " in button code
load new pdb, orient it
zap; load ../pdbs/1acx.pdb; rotate y 90;
zoom 150;
show S-S bonds
select cys88, cys83;
wireframe 100; ssbonds on;
color S-S bonds purple, thicken S-S bonds
color ssbonds [XFF00FF]; ssbonds 50
remove S-S bonds
ssbonds off;
make an arbitrary bond between atom #509 and #638
monitor 509 638;
remove distance label
set monitor off;
restore distance label
set monitor on;
remove arbitrary bond
monitor off;
load new pdb, show hydrogen bonds
load ../pdbs/1dc7.pdb; hbonds on;
color hydrogen bonds green, thicken hbonds
color hbonds [X33FF00]; hbonds 50
remove hydrogen bonds
hbonds off;
[I. Introduction] [II. Display] [III. Loading and Positioning]
[IV. The Select Command and Labeling] [V. Coloring and Schemes]
[VI. Illustrating Bonds] [VII. Animation]
VII. Animation
Animations are sometimes superior to the rotations and translations discussed previously
because animations can cause the molecule at hand to move or change position in a smooth
fashion. Coupled with creative displays and coloration, animation commands can be employed to
great effect in illustrating key points of molecular structure.
One of the most essential animation commands is "move". "Move" is followed by a set of
numbers that quantify a set of animation parameters. Here we describe the use of the first nine
such parameters, i.e.: "move _ _ _ _ _ _ _ _ _ ", where each of the nine spaces specifies the
degree of an animation parameter.
The parameters for each space following a "move" command (in order) are:
1
2
3
4
5
6
7
8
9
Xrot YRot ZRot Zoom XTrans YTrans ZTrans Slab TotalTime
The first three parameters are rotations around the X, Y and Z axes. Fourth is the zoom modifier,
expressed in positive (zoom in) or negative (zoom out) numbers. Note that in a "move" command,
zoom values are not expressed in percentages of the original, unlike the use of "zoom" as a stand
alone script command. The next three parameters (5,6 and 7) deal with translation along the
three axes (7, Z translation, is not functional - always use zero in that slot). Note: contrary to
intuition, positive numbers for Y translation move molecules down and negative numbers move
molecules up. 8th is the slab parameter. Slab "slices" the molecule, i.e. removes atoms down to a
specified depth so that interior features may be easily observed. Parameter 9 is the amount of
time (in seconds) to take in performing the previous move commands. It is important to allow
sufficient time for the animation so as not to disorient the viewer. Contrariwise, too long an
animation can prove tedious. There are two other move parameters, Frames/Second and
MaximumAcceleration that can be specified in the 10th and 11th positions (not considered here).
"Move" is used in some of Chime's most impressive animations and provides great versatility,
especially when coupled with "delay". "Delay" pauses the Chime script for a specified amount of
time before the next command is executed. "Delay" is specified in seconds, e.g. "delay 5" causes
a pause of five seconds. In addition to use in animations, "delay" can be an effective tool in a
variety of display and coloration contexts.
The "spin" command evokes a continuous animation. SpinX, spinY, and spinZ are used to spin a
molecule around a particular axis. The spin command is followed by a value that specifies the
rate of spinning in degrees/second. Spiny is often used when loading a molecule. Caution must
be used in spinning a molecule because when later "move" commands are executed, they will
take effect from whatever arbitrary position the molecule happens to be in (spinning). This can be
acceptable, but can also muddy a point because the molecule will not be oriented correctly. One
solution is the use of a "view restore" (see Loading and Positioning, above) command just prior to
"move", but this approach can lead to a jarring reorientation of the molecule. We have found it
useful, in the initial loading of a pdb, to follow a "spiny=20" command with a "startspin=false"
command, which disables the spinning of the molecule. A later Chime script can be used to start
the molecule spinning, using the "spin" command. A new (9/2001) Chime resource, MoveTo, is
quite useful in smoothly restoring a molecule to a desired orientation. See the MoveTo home
page of Carlson and Wells.
Changes in display (e.g. wireframe thickness), separated by brief delays, can be used to "build
up" or "dissolve" molecules to provide smooth, animated transitions in rendering.
Blinking can be used to draw attention to particular molecular features (e.g. bonding partners).
Blinking is achieved by causing the feature to flash on and off or to expand and contract a few
times, using appropriate display commands separated by delays.
Animation Commands
Buttons
code for button = <embed type = "application/x-spt"
width=15 height=15 button=followed
target="molecule" script="Chime Scripts
Here"></embed>
Chime Scripts in buttons
Cut and paste in " " in button code
load new pdb
zap; load ../pdbs/synth3atp.pdb;
rotate x 90º, pause for a second, rotate back
move 90 0 0 0 0 0 0 0 3; delay 1;
move -90 0 0 0 0 0 0 0 3;
rotate y 90º, pause for a second, rotate back
move 0 90 0 0 0 0 0 0 3; delay 1;
move 0 -90 0 0 0 0 0 0 3;
rotate z 90º, pause for a second, rotate back
move 0 0 90 0 0 0 0 0 3; delay 1;
move 0 0 -90 0 0 0 0 0 3;
zoom in 100, pause for 2 seconds, zoom out
move 0 0 0 100 0 0 0 0 5; delay 2;
move 0 0 0 -100 0 0 0 0 5;
translate x 25, pause for a second, translate back
move 0 0 0 0 25 0 0 0 5; delay 1;
move 0 0 0 0 -25 0 0 0 5;
translate y 25, pause for a second, translate back
move 0 0 0 0 0 25 0 0 5; delay 1;
move 0 0 0 0 0 -25 0 0 5;
slab 5 , rotate y 45º,pause for half a second, rotate
back, slab off
move 0 0 0 0 0 0 0 15 3; move 0 45 0
0 0 0 0 0 3; delay .5; move 0 -45 0 0 0
0 0 0 3; slab off;
select amino acid 509, simultaneous rotation of all 3
axis plus zoom and translation, pause for a few
seconds, return to original oreientation/display
select 509; wireframe 75; dots 100;
move 92 -47 5 63 7 -13 2 0 5; delay 2;
move -92 47 -5 -63 -7 13 -2 0 5; delay
1; wireframe; dots off;
spin on
view save 2; spin on;
spin off
spin off; delay 1; view restore 2;
spin 360º in 8 seconds
move 0 360 0 0 0 0 0 0 8;
building up using wireframe display only
select all; wireframe 1; delay .3;
wireframe 5; delay .3; wireframe 10;
delay .3; wireframe 20; delay .3;
wireframe 40; delay .3; wireframe 60;
delay .3; wireframe 100; delay .3;
wireframe 160;
building up using both wireframe and spacefill
displays
select amino, nucleic; wireframe 1;
delay .3; wireframe 5; delay .3;
wireframe 10; delay .3; wireframe 20;
delay .3; wireframe 40; delay .3;
wireframe 60; delay .3; wireframe
100; delay .3; wireframe off; spacefill
125; delay .3; spacefill 200; delay .3;
spacefill 250; delay .3; spacefill;
move 92 -47 5 63 7 -13 2 0 5; select
water; spacefill off; select 509; delay
.5; spacefill 200; delay .3;
wireframe 200; spacefill off; delay .3;
wireframe 150; delay .3; select
protein, nucleic, ligand; spacefill 300;
select 509; color cpk; spacefill off;
wireframe 150; delay .3; select
protein, nucleic, ligand; color
[XCCCCCC]; spacefill 150; trace 150;
dissolving to show or emphasize a particular group or
wireframe off; select 509; color cpk;
residue
spacefill off; wireframe 150; delay .3;
select protein, nucleic, ligand; color
[XCCCCCC]; spacefill off; trace 100;
select 509; color cpk; spacefill off;
trace off; wireframe 100; delay .3;
select protein, nucleic, ligand; color
[XCCCCCC]; trace 50; select 509;
color cpk; spacefill off; trace off;
wireframe 100; delay .5; move -92 47
-5 -63 -7 13 -2 0 5
blinking H bond
move 0 0 0 100 0 15 0 0 5; select 506;
wireframe 150; color cpk; move 0 75 0
0 0 0 0 0 3; monitor 3969 3949; set
monitor off; delay .5; select
atomno=3969, atomno=3949; spacefill
300; delay .5; spacefill off; delay .5;
spacefill 300; delay .5; spacefill off;
delay .5; spacefill 300; delay .5;
spacefill off
[I. Introduction] [II. Display] [III. Loading and Positioning]
[IV. The Select Command and Labeling] [V. Coloring and Schemes]
[VI. Illustrating Bonds] [VII. Animation]
Back to Introduction
Back to the OMM Exhibits
Feedback to David Marcey: marcey@clunet.edu