Command List

Command usage of jV follows that of Rasmol with some modifications. In the following part, command arguments that can take an arbitrary value are denoted as for example, arguments restricted to several possible values are listed with / as a delimiter, and arguments that can be omitted are put in brackets {}. Commands, exit, load, quit, save, script, and write, are not available in applet circumstance.

add_backboe
add_backbone { {}} Adds backbone atom names to predefined ones for the specified residue. The  is a comma-delimited list of atom names. Omitting the  means to reset the residue to the initial setting. When no arguments are given, the current settings are shown.

anim
anim forward { } Starts animation forward. If the is given, just move frames forward by the specified amount.

anim backward { } Starts animation backward. If the is given, just move frames backward by the specified amount.

anim stop Stops animation.

animframe
animframe {} Sets the frame of all animation files for the specified value. When  is given, only the specified file is processed.

animmode
animmode once Sets the behavior of animation for 'once'. When the frame reaches the last one, animation is stopped.

animmode loop Sets the behavior of animation for 'loop'. When the frame reaches the last one, animation is reset to the first frame and continues playing.

animmode swing Sets the behavior of animation for 'swing'. When the frame reaches the last one, the direction of animation is reversed.

animrange
animrange - {} Sets the range of all animation files. When is given, only the specified file is processed.

animselect
animselect {-a/-r}  Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

animspeed
animspeed Sets the animation speed. The argument should be an integer value from 1 to 20.

animstep
animstep {} Sets the step of all animation files for the specified value. When  is given, only the specified file is processed.

backbone
backbone {on/true} Turns on the selected backbone bonds.

backbone off/false Turns off the selected backbone bonds.

backbone Turns on the selected backbone bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

background
background Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

ball_and_stick
ball_and_stick {on/true} Turns on the ball and stick image of the selected atoms with ball radius 0.5 and stick radius 0.2 in angstrom.

ball_and_stick off/false Turns off the ball and stick image of the selected atoms.

ball_and_stick   Turns on the ball and stick image of the selected atoms with the specified ball radius and stick radius (angstrom or Rasmol unit). The maximum parameter value is 3.0 and 2.0, respectively.

cartoon
cartoon {on/true} Turns on the thick ribbons for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

cartoon off/false Turns off the thick ribbons for the selected residues.

cartoon  Turns on the thick ribbons for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

center
center {-r/-s} {} Sets the center of rotation and the center of the screen to the center of a group of atoms specified by the atom expression. When the option -r or -s is specified, only the center of rotation or the center of the screen is modified, respectively.

center {-r} [x, y, z] Moves the center of rotation and the center of the screen from the current position by the specified amount. When the option -r is specified, only the center of rotation is modified.

center {-r} {x, y, z} Sets the center of rotation and the center of the screen to the specified coordinates. When the option -r is specified, only the center of rotation is modified.

center -s [x, y] Moves the center of the screen from the current position by the specified amount.

center -s {x, y} Sets the center of the screen to the specified coordinates.

color
color {atoms} Sets the color of the selected atoms. The color may be given as RGB values [r,g,b], predefined color names, or predefined color schemes; amino, chain, charge, cpk, group, shapely, structure, and temperature.

color bonds/backbone/ribbons/hbonds/ssbonds Sets the color of the specified object. The color may be given as RGB values [r,g,b] or predefined color names. For hydrogen bonds, color scheme 'type' can be specified.

color bonds/backbone/ribbons/hbonds/ssbonds none Resets the color of the specified object.

colorvertex
colorvertex Sets the color of the selected vertices. The color may be given as RGB values [r,g,b] or predefined color names.

colorvertex none Resets the color of the selected vertices.

cpk
cpk A synonym of the spacefill command.

define
define <atom_expression> Associates an arbitrary set of atoms specified by the atom expression with a unique name.

display
display all Displays the image of all files.

display none Turns off the image of all files.

display {-a/-r} <file_IDs> Displays the image of the specified files and turns off the others. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, turns the image of the specified files on or off, respectively, and the others remain unchanged.

displayatom
displayatom {on/true} Displays the selected atoms.

displayatom off/false Turns off the selected atoms.

displayvertex
displayvertex {on/true} Displays the selected vertices.

displayvertex off/false Turns off the selected vertices.

echo
echo Echoes the specified message back to the message area.

exit
exit Terminates the application.

fit
fit <file1_ID> <file2_ID> Sets the transform matrix of file1 identical to that of file2.

fselect
fselect all Selects all files.

fselect none Selects no files.

fselect {-a/-r} <file_IDs> Selects the specified files and makes the others not selected. More than one file IDs can be specified by putting commas as the delimiter. When the option -a or -r is specified, only the selection status of the specified files are modified, selected or not selected, respectively, and the others remain unchanged.

hbonds
hbonds {on/true} Turns on the selected hydrogen bonds.

hbonds off/false Turns off the selected hydrogen bonds.

hbonds Turns on the selected hydrogen bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

load
load {pdbml} {fit <file_ID>} {biomolecule <assembly_ID>} {filter <atom_expression>} Opens a PDBML file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

load mmcif {fit <file_ID>} {biomolecule <assembly_ID>} {filter <atom_expression>} Opens a mmCIF file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

load pdb {fit <file_ID>} {filter <atom_expression>} Opens a PDB file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

load polygon {fit <file_ID>} Opens a polygon file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'.

load polygon_cgo {fit <file_ID>} Opens a polygon CGO file distributed at eF-site system. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'.

load animation {fit <file_ID>} {filter <atom_expression>} Opens an animation file. URL can be used to open a remote file. The transform matrix is copied from the file specified by 'fit'. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

load ftp <PDB_code> {fit <file_ID>} {biomolecule <assembly_ID>} {filter <atom_expression>} Retrieves a PDBML file from the PDBj FTP site and opens it. The transform matrix is copied from the file specified by 'fit'. A biomolecule structure can be specified by 'biomolecule'. For a biomolecule structure, a distinct model ID is assigned to each transform operation, which is listed by 'show information' command. Only atoms that matches a given filter are loaded. The filter takes any atom expressions except some keywords (bonded, helix, sheet, turn, within and pdbj:). The atom expression should be double-quoted or enclosed in a parenthesis when it contains spaces.

load efsite <efsite_ID> Retrieves the PDB file and efvet file from eF-site database.

pause
pause Stops the execution of a script file until any key is pressed to restart.

pdbj_describe
pdbj_describe <file_id> { } Shows the document for the jV_command in PDBMLplus specified by file ID and name. When the name is not specified, all available names are listed.

pdbj_execute
pdbj_execute <file_id> Executes the jV_command in PDBMLplus specified by file ID and name.

quit
quit A synonym of the exit command.

refresh
refresh Redraws all images.

default
reset Restores the original viewing transformation of all images, the center of rotation, and the view point.

cartoon
reset cartoon Restores the thickness of the cartoon representation.

line_width
reset line_width Restores the width of lines in polygon images.

pickradius
reset pickradius Restores the mouse-pickable region of each atom.

point_size
reset point_size Restores the size of points in polygon images.

polyline_width
reset polyline_width Restores the width of polylines in polygon images.

transparency
reset transparency Restores the transparency of polygon images.

reset point_transparency Restores the transparency of points in polygon images.

reset line_transparency Restores the transparency of lines in polygon images.

reset triangle_transparency Restores the transparency of triangles in polygon images.

reset quad_transparency Restores the transparency of quads in polygon images.

reset polyline_transparency Restores the transparency of polylines in polygon images.

ribbons
ribbons {on/true} Turns on the ribbon surfaces for the selected residues. When a chain does not have enough atoms to draw the ribbon model, a backbone will be shown instead.

ribbons off/false Turns off the ribbon surfaces for the selected residues.

ribbons <half_width> Turns on the ribbon surfaces for the selected residues with the specified half width (angstrom or Rasmol unit). The maximum parameter value is 4.0.

rotate
rotate x/y/z Rotates images about the specified axis by the specified angle in degrees.

save
save {pdb} Saves the currently selected set of atoms in a PDB format file.

save mmcif Saves the currently selected set of atoms in a mmCIF format file.

save script Creates a script file that reproduces the currently displayed image.

save png Creates a PNG image file of the currently displayed image.

save jpeg { } Creates a JPEG image file of the currently displayed image. The compression quality can be specified, 0 < quality <= 1, where 'quality = 1' means no compression.

script
script Opens and executes the specified script file. URL can be used to open a remote file.

select
select Selects all atoms. Whether hetero atoms and hydrogens are selected or not depends on the internal parameters, hetero and hydrogen, respectively.

select all Selects all atoms including hetero atoms and hydrogens.

select none Selects no atoms.

select <atom_expression> Selects a group of atoms specified by the atom expression.

selectvertex
selectvertex {all} Selects all vertices.

selectvertex none Selects no vertices.

selectvertex <vertex_expression> Selects a group of vertices specified by the vertex expression.

ambient
set ambient { } Sets the amount of ambient light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 33.

adjustview
set adjustview on The view point is automatically adjusted when a new file is loaded.

set adjustview off The view point is kept unchanged when a new file is loaded.

background
set background Changes the background color. The color may be given as RGB values [r,g,b], or predefined color names.

bondmode
set bondmode and Specifies how to select an individual bonds. A bond is selected when both atoms connected by the bond are selected.

set bondmode or Specifies how to select an individual bonds. A bond is selected when either of the connected atoms is selected.

cartoon
set cartoon { } Specifies the thickness of the cartoon representation (angstrom or Rasmol unit). The maximum parameter value is 2.0. When the parameter is not specified, it is restored to the default value.

cartoon_loop_tube
set cartoon_loop_tube on The loop region is drawn as tube in the cartoon representation.

set cartoon_loop_tube off The loop region is drawn as square pillar in the cartoon representation.

cartoon_round
set cartoon_round on Square pillar with round edge is drawn in the cartoon representation (except beta strands).

set cartoon_round off Square pillar is drawn in the cartoon representation.

center
set center <atom_expression> Sets the default center of the selected files to the center of a group of atoms specified by the atom expression.

set center [x, y, z] Sets the default center of the selected files to the specified coordinates.

diffuse1
set diffuse1 { } Sets the amount of the first diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

diffuse1_direction
set diffuse1_direction {[x, y, z]} Sets the direction of the first diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

diffuse2
set diffuse2 { } Sets the amount of the second diffuse light. The value must be between 0 and 100. When the parameter is not specified, it is restored to the default value 50.

diffuse2_direction
set diffuse2_direction {[x, y, z]} Sets the direction of the second diffuse light. When the parameter is not specified, it is restored to the default value [-1, -1, -1].

drawlevel
set drawlevel Specifies precision of the rendering of spheres and cylinders. The value may be given as an integer (minimum 5) that stands for the number of straight line segments to represent an arc of 180 degrees.

efsite_url
set efsite_url <URL> Sets the URL for eF-site.

ext_site_url
set ext_site_url <URL> Sets the URL for an external database site.

hbonds
set hbonds backbone Hydrogen bonds are displayed between backbones.

set hbonds sidechain Hydrogen bonds are displayed between sidechains.

hetero
set hetero on Sets the default behavior of the select command such that hetero atoms are selected.

set hetero off Sets the default behavior of the select command such that hetero atoms are not selected.

hydrogen
set hydrogen on Sets the default behavior of the select command such that hydrogens are selected.

set hydrogen off Sets the default behavior of the select command such that hydrogens are not selected.

imagesize
set imagesize Sets the size of the 3D-rendering panel in pixels. The size will be set within the screen size with the width being an even integer.

line_width
set line_width Sets the width of lines in polygon images. The should be larger than 0.

loadcenter
set loadcenter on When a file is opened, sets the default center of that file to the center of all files that have already opened.

set loadcenter off When a file is opened, sets the default center of that file according to its own coordiantes.

pdbml_noatom_url
set pdbml_noatom_url <URL> Sets the URL for PDBML noatom files.

pdbml_extatom_url
set pdbml_extatom_url <URL> Sets the URL for PDBML extatom files.

pdbml_plus_url
set pdbml_plus_url <URL> Sets the URL for PDBMLplus files.

picking
set picking off Turns off the mouse picking.

set picking ident Sets the mouse picking behavior to show atom identification.

set picking coord Sets the mouse picking behavior to show atom coordinates with identification.

set picking distance Sets the mouse picking behavior to show the distance between atoms successively picked. Rotation and translation of molecules between two mouse pickings do not affect the distance measurement.

set picking center Sets the mouse picking behavior to specify the center of rotation and center of the screen.

set picking select Sets the mouse picking behavior to select the file that contains the atom picked.

pickradius
set pickradius Sets the mouse-pickable region of each atom to be the sphere centered to each atom with the specified radius (angstrom or Rasmol unit).

point_size
set point_size Sets the size of points in polygon images. The should be larger than 0.

polyline_width
set polyline_width Sets the width of polylines in polygon images. The should be larger than 0.

projection
set projection perspective Sets the projection mode for a perspective projection.

set projection parallel { } Sets the projection mode for a parallel projection. The size of image (fit to the height of the screen) can be specified (angstrom or Rasmol unit).

ribbonback
set ribbonback Sets the color of the back of ribbon models. The color may be given as RGB values [r,g,b] or predefined color names.

set ribbonback none Resets the color of the back of ribbon models.

specular
set specular on/true Enables the display of specular highlights on solid objects.

set specular off/false Disables the display of specular highlights on solid objects.

set specular Enables the display of specular highlights on solid objects. The value between 0 and 100 specifies the specular color in gray scale with 0 and 100 being black and white, respectively. The default value is 50.0.

specpower
set specpower Sets the shininess of solid objects. The value between 0 and 100 specifies a material reflection coefficient with 0 being diffuse surfaces and 100 being shiny surfaces.

ssbonds
set ssbonds backbone Disulfide bonds are displayed between backbones.

set ssbonds sidechain Disulfide bonds are displayed between sidechains.

stereo
set stereo A synonym of the stereo command.

transparency
set transparency Sets the transparency of polygon images.

set point_transparency Sets the transparency of points in polygon images.

set line_transparency Sets the transparency of lines in polygon images.

set triangle_transparency Sets the transparency of triangles in polygon images.

set quad_transparency Sets the transparency of quads in polygon images.

set polyline_transparency Sets the transparency of polylines in polygon images.

viewpoint
set viewpoint {x, y, z} Sets the viewpoint to the specified coordinates.

show
show godata Displays gene ontology data of molecules.

show imagesize Displays the size of the 3D-rendering panel.

show information Displays a detail discription of molecules.

show site { :<db>: } Displays site information in an external database.

show transform Displays the transform matrix of molecules.

show viewpoint Displays the current viewpoint.

show pdbj Displays keywords available in PDBj expression.

slab
slab {on/true} Enables the z-clipping plane of molecules and polygons.

slab off/false Disables the z-clipping plane of molecules and polygons.

slab Sets the position of the z-clipping plane of molecules and polygons. The parameter may be given as a number from 0 to 100. The values 0 and 100 represent that image as a whole is completely invisible and visible, respectively.

slab -v Sets the position of the z-clipping plane of molecules and polygons by specifying the z coordinate value.

spacefill
spacefill {on/true} Turns on the ball image of the selected atoms.

spacefill off/false Turns off the ball image of the selected atoms.

spacefill Turns on the ball image of the selected atoms with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 3.0.

spacefill temperature Turns on the ball image of the selected atoms using the temperature factor as radius.

ssbonds
ssbonds {on/true} Turns on the selected disulfide bonds.

ssbonds off/false Turns off the selected disulfide bonds.

ssbonds Turns on the selected disulfide bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

stereo
stereo {on/true} Enables stereo display. This command without arguments cycles three state; 'stereo off', 'stereo on' in cross-eyed mode and 'stereo on' in parallel-eyed mode.

stereo off/false Disables stereo display.

stereo Enables stereo display with the specified separation angle. Positive and negative values represent cross-eyed and parallel-eyed viewing, respectively.

structure
structure Estimates the secondary structure using Kabsch and Sander's DSSP algorithm.

trace
trace {on/true} Turns on a tube representation for the selected residues. When a chain does not have enough atoms to draw the tube model, a backbone will be shown instead.

trace off/false Turns off a tube representation for the selected residues.

trace Turns on a tube representation for the selected residues with the specified radius (angstrom or Rasmol unit). The maximum parameter value is 2.0.

translate
translate x/y/z Moves images along the specified axis by the specified amount (angstrom).

wireframe
wireframe {on/true} Turns on the selected bonds.

wireframe off/false Turns off the selected bonds.

wireframe Turns on the selected bonds with the specified raidus (angstrom or Rasmol unit). The maximum parameter value is 2.0.

write
write A synonym of the save command.

zap
zap {<file_IDs>} Closes the specified files. More than one file IDs can be specified by putting commas as the delimiter. When the paraneter is absent, all files are closed.

zoom
zoom { } Sets the magnification of the image as a whole. The value stands for the magnification as a percentage of the current scale. The minimum parameter value is 10.0.