jV Manual

2.1. add_backbone

add_backbone {<residue_name> {<atom_names>}}

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

2.2. anim

anim forward {<value>}

Starts animation forward. If the <value> is given, just move frames forward by the specified amount.

anim backward {<value>}

Starts animation backward. If the <value> is given, just move frames backward by the specified amount.

anim stop

Stops animation.

2.3. animframe

animframe <frame> {<file_ID>}

Sets the frame of all animation files for the specified value. When <file_ID> is given, only the specified file is processed.

2.4. 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.

2.5. animrange

animrange <init_frame>-<term_frame> {<file_IDs>}

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

2.6. animselect

animselect {-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.

2.7. animspeed

animspeed <speed>

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

2.8. animstep

animstep <step> {<file_ID>}

Sets the step of all animation files for the specified value. When <file_ID> is given, only the specified file is processed.

2.9. backbone

backbone {on/true}

Turns on the selected backbone bonds.

backbone off/false

Turns off the selected backbone bonds.

backbone <radius>

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

2.10. background

background <color>

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

2.11. 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 <ball_radius> <stick_radius>

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..

2.12. 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 <half_width>

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.

2.13. center

center {-r/-s} {<atom_expression>}

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.

2.14. color

color {atoms} <color>

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/ribbonback <color>

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/ribbonback none

Resets the color of the specified object.

2.15. colorvertex

colorvertex <color>

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.

2.16. cpk

cpk

A synonym of the spacefill command.

2.17. define

define <name> <atom_expression>

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

2.18. 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.

2.19. displayatom

displayatom {on/true}

Displays the selected atoms.

displayatom off/false

Turns off the selected atoms.

2.20. displayvertex

displayvertex {on/true}

Displays the selected vertices.

displayvertex off/false

Turns off the selected vertices.

2.21. echo

echo <string>

Echoes the specified message back to the message area.

2.22. exit

exit

Terminates the application.

2.232. fit

fit <file1_ID> <file2_ID>

Sets the transform matrix of file1 identical to that of file2.

2.24. fselect

fselect all

Selects all files.

fselect none

Selects no files.

fselect {-a/-r} <file_IDs>

2.25. hbonds

hbonds {on/true}

Turns on the selected hydrogen bonds.

hbonds off/false

Turns off the selected hydrogen bonds.

hbonds <radius>

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

2.26. load

load {pdbml} <filename> {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 <filename> {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 <filename> {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 <filename> {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 <filename> {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 <filename> {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.

2.27. pause

pause

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

2.28. pdbj_describe

pdbj_describe <file_id> {<name>}

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.

2.29. pdbj_execute

pdbj_execute <file_id> <name>

Executes the jV_command in PDBMLplus specified by file ID and name.

2.30. quit

quit

A synonym of the exit command.

2.31. refresh

refresh

Redraws all images.

2.32 reset

2.32.1 default

reset

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

2.32.2 cartoon

reset cartoon

Restores the thickness of the cartoon representation.

2.32.3 line_width

reset line_width

Restores the width of lines in polygon images.

2.32.4 pickradius

reset pickradius

Restores the mouse-pickable region of each atom.

2.32.5 point_size

reset point_size

Restores the size of points in polygon images.

2.32.6 polyline_width

reset polyline_width

Restores the width of polylines in polygon images.

2.32.7 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.

2.33. 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.

2.34. rotate

rotate x/y/z <angle>

Rotates images about the specified axis by the specified angle in degrees.

2.35. save

save {pdb} <filename>

Saves the currently selected set of atoms in a PDB format file.

save mmcif <filename>

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

save script <filename>

Creates a script file that reproduces the currently displayed image.

save png <filename>

Creates a PNG image file of the currently displayed image.

save jpeg <filename> {<quality>}

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.

2.36 script

script <filename>

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

2.37 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.

2.38. selectvertex

selectvertex {all}

Selects all vertices.

selectvertex none

Selects no vertices.

selectvertex <vertex_expression>

Selects a group of vertices specified by the vertex expression.

2.39 set

2.39.1 ambient

set ambient {<value>}

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.

2.39.2 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.

2.39.3 background

set background <color>

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

2.39.4 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.

2.39.5 cartoon

set cartoon {<value>}

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.

2.39.6 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.

2.39.7 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.

2.39.8 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.

2.39.9 diffuse1

set diffuse1 {<value>}

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.

2.39.10 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].

2.39.11 diffuse2

set diffuse2 {<value>}

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.

2.39.12 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].

2.39.13 drawlevel

set drawlevel <value>

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.

2.39.14 efsite_url

set efsite_url <URL>

Sets the URL for eF-site.

2.39.15 ext_site_url

set ext_site_url <prefix> <URL>

Sets the URL for an external database site.

2.39.16 hbonds

set hbonds backbone

Hydrogen bonds are displayed between backbones.

set hbonds sidechain

Hydrogen bonds are displayed between sidechains.

2.39.17 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.

2.39.18 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.

2.39.19 imagesize

set imagesize <width> <height>

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.

2.39.20 line_width

set line_width <value>

Sets the width of lines in polygon images. The <value> should be larger than 0.

2.39.21 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.

2.39.22 pdbml_noatom_url

set pdbml_noatom_url <URL>

Sets the URL for PDBML noatom files.

2.39.23 pdbml_extatom_url

set pdbml_extatom_url <URL>

Sets the URL for PDBML extatom files.

2.39.24 pdbml_plus_url

set pdbml_plus_url <URL>

Sets the URL for PDBMLplus files.

2.39.25 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.

2.39.26 pickradius

set pickradius <value>

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

2.39.27 point_size

set point_size <value>

Sets the size of points in polygon images. The <value> should be larger than 0.

2.39.28 polyline_width

set polyline_width <value>

Sets the width of polylines in polygon images. The <value> should be larger than 0.

2.39.29 projection

set projection perspective

Sets the projection mode for a perspective projection.

set projection parallel {<size>}

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).

2.39.30 ribbonback

set ribbonback <color>

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.

2.39.31 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 <value>

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.

2.39.32 specpower

set specpower <value>

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.

2.39.33 ssbonds

set ssbonds backbone

Disulfide bonds are displayed between backbones.

set ssbonds sidechain

Disulfide bonds are displayed between sidechains.

2.39.34 stereo

set stereo

A synonym of the stereo command.

2.39.35 transparency

set transparency <value>

Sets the transparency of polygon images.

set point_transparency <value>

Sets the transparency of points in polygon images.

set line_transparency <value>

Sets the transparency of lines in polygon images.

set triangle_transparency <value>

Sets the transparency of triangles in polygon images.

set quad_transparency <value>

Sets the transparency of quads in polygon images.

set polyline_transparency <value>

Sets the transparency of polylines in polygon images.

2.39.36 viewpoint

set viewpoint {x, y, z}

Sets the viewpoint to the specified coordinates.

2.40. show

show efsite_url

Displays the URL for eF-site.

show ext_site_url

Displays the URL for external database sites.

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 pdbml_url

Displays the URL for PDBML files.

show site {<prefix>:<db>:<category>}

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.

2.41. 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 <ratio>

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 <value>

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

2.42. 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 <radius>

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.

2.43. ssbonds

ssbonds {on/true}

Turns on the selected disulfide bonds.

ssbonds off/false

Turns off the selected disulfide bonds.

ssbonds <radius>

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

2.44. stereo

stereo {redblue/redcyan/redgreen} <angle>

Enables stereo display with the specified separation angle. Positive and negative values represent wall-eyed and cross-eyed viewing, respectively. When 'redblue', 'redcyan' or 'redgreen' is passed as the first argument, anaglyph 3D is rendered with red-blue, red-cyan or red-green color pair, respectively.

stereo {on/true/redblue/redcyan/redgreen}

Enables side-by-side stereo viewing (for argument 'on' or 'true') or anaglyph 3D rendering (for argument 'redblue', 'redcyan' or 'redgreen') with a previously specified separation angle, where program's initial value is 6 degrees. The command without arguments cycles six states; wall-eyed stereo, cross-eyed stereo, red-blue anaglyph, red-cyan anaglyph, red-green anaglyph and stereo-off.

stereo off/false

Disables stereo display.

2.45. structure

structure

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

2.46. 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 <radius>

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

2.47. translate

translate x/y/z <value>

Moves images along the specified axis by the specified amount (angstrom).

2.48. wireframe

wireframe {on/true}

Turns on the selected bonds.

wireframe off/false

Turns off the selected bonds.

wireframe <radius>

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

2.49. write

write

A synonym of the save command.

2.50. 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.

2.51. zoom

zoom {<value>}

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.

3.1. predefined set

3.1.1 element name

Element names, such as carbon or nitrogen, can be used to select atoms.

3.1.2 set based on residue property

a) amino acids in protein molecule

	ALA	ARG	ASN	ASP	CYS	GLU	GLN	GLY	HIS	ILE	LEU	LYS	MET	PHE	PRO	SER	THR	TRP	TYR	VAL
Acidic				*		*
Acyclic	*	*	*	*	*	*	*	*		*	*	*	*			*	*			*
Aliphatic	*							*		*	*									*
Aromatic									*					*				*	*
Basic		*							*			*
Buried	*				*					*	*		*	*				*		*
Charged		*		*		*			*			*
Cyclic									*					*	*			*	*
Hydrophobic	*							*		*	*		*	*	*			*	*	*
Large		*				*	*		*	*	*	*	*	*				*	*
Medium			*	*	*										*		*			*
Negative				*		*
Neutral	*		*		*		*	*	*	*	*		*	*	*	*	*	*	*	*
Polar		*	*	*	*	*	*		*			*				*	*
Positive		*							*			*
Small	*							*
Surface		*	*	*		*	*	*	*			*			*	*	*		*
Cysteine					*
Amino	above 20 amino acids + other amino acids
Protein	above 'Amino' set + UNK, ACE + FOR (PDB version 2.3 only)

Here, 'other amino acids' stands for components whose type is one of the followings in Chemical Component Dictionary.

D-PEPTIDE LINKING
D-PEPTIDE NH3 AMINO TERMINUS
L-PEPTIDE COOH CARBOXY TERMINUS
L-PEPTIDE LINKING
L-PEPTIDE NH3 AMINO TERMINUS
PEPTIDE LINKING
PEPTIDE-LIKE

b1) nucleotides (for PDB version 2.3)

	A	C	G	T	U	+U	I	1MA	5MC	OMC	1MG	2MG	M2G	7MG	OMG	YG	H2U	5MU	PSU
AT	*			*
CG		*	*
Purine	*		*
Pyrimidine		*		*
DNA	*	*	*	*
RNA	*	*	*		*	*	*	*	*	*	*	*	*	*	*	*	*	*	*
Nucleic	*	*	*	*	*	*	*	*	*	*	*	*	*	*	*	*	*	*	*

b2) nucleotides (for PDB version 3)

	DA	DC	DG	DT	A	C	G	U	other DNA	other RNA
AT	*			*
CG		*	*
Purine	*		*		*		*
Pyrimidine		*		*		*		*
DNA	*	*	*	*					*
RNA					*	*	*	*		*
Nucleic	*	*	*	*	*	*	*	*	*	*

Here, 'other DNA' and 'other RNA' stand for components whose type is DNA LINKING and RNA LINKING respectively in Chemical Component Dictionary.

c) others

	HOH	DOD	SO4	PO4
Water	*	*
Ions			*	*
Solvent	*	*	*	*

3.1.2 others

Alpha	atoms whose name is CA.
Hetero	atoms written as HETATM in PDB files or atoms in Solvent set.
Ligand	atoms in Hetero set and not in Solvent set.
Backbone Mainchain	atoms in Amino set whose name is N, CA, C or O, or atoms in Nucleic set whose name is P,O1P,O2P,O5,C5,C4,O4,C3,O3,C2,O2 or C1*.
Sidechain	atoms in Amino set or Nucleic set and not in Backbone set.
Alphaphospho	atoms in Protein set whose name is CA or atoms in Nucleic set whose name is P.
Bonded	atoms that is connected to at least one other atom.
Selected	atoms currently selected.
Helix	atoms in the alpha-helix structure.
Sheet	atoms in the beta-sheet structure.
Turn	atoms in the turn structure.

3.2. comparison operators

Parts of a molecule can be selected using equality, inequality and ordering operators on their properties. Possible operators are =, ==, <>, !=, /=, <, <=, > and >=, and possible property names are as follows.

AtomNo	atom ID in PDB files.
ElemNo	atomic number.
ResNo	residue ID in PDB files.
Radius	radius of a ball image of atoms.
Temperature	temperature factor of atoms.
Model	model ID in PDB files.
File	File ID.

3.3. residue range

A group of atoms in a molecule can be selected by the residue ID. For example, command 'select 3' selects atoms whose residue ID is 3, and 'select 3-10' selects atoms whose residue ID is larger than or equal to 3 and smaller than or equal to 10. Optionally, the chain ID can be specified after residue range with a colon. For example, command 'select 3:A' selects atoms whose residue ID is 3 in the A chain. The chain ID can be specified in several ways (see primitive expression).

3.4. within expression

A within expression selects atoms that exist within a specified distance from another set of atoms. For example, 'select within(3.0, backbone) selects atoms within a 3.0 Angstrom radius of any atom in a protein or nucleic acid backbone.

3.5. PDBj expression

A PDBj expression selects a group of atoms according to molecule's properties defined in the PDBMLplus file. It takes the following form;

pdbj:keyword.

For example, 'select pdbj:binding'. The keywords available for each molecule are obtained by the 'show pdbj' command.

3.6. primitive expression

A primitive expression takes such a form as

'residue name [residue ID][:chain ID][.atom name][;alternate location][/model ID][@file ID]'.

Here, residue name and atom name are three letter and four letter name, respectively, and terms in square brackets can be omitted. For example, command 'select SER.CA' selects all alpha carbon atoms in serine. Residue names that contain numeric characters should be enclosed in square brackets such as '[SO4]'. Expressions are treated in a case-insensitive manner. However, the chain ID can be specified case-sensitively such as 'a_A' or 'a_a', where these mean the chains whose auth_asym_id is 'A' or 'a', respectively. In the same way, you can use label_asym_id to specify chains case-sensitively such as 'l_A'. Note that the label_asym_id is available only for PDBML files and not for PDB flat files.

4. Vertex Expression

In order to specify a group of vertices in a polygon, the following three expressions are available.

4.1. comparison operators
4.2. within expression
4.3. box expression

The standard boolean connectives 'and', 'or' and 'not', and brackets can be used to construct a complex expression. The boolean connectives may be abbreviated as '&', '|', and '!', respectively.

4.1. comparison operators

Parts of a polygon can be selected using equality and inequality operators on the ID numbers assigned to each vertex; for example, id >= 100. Possible operators are =, ==, <>, !=, /=, <, <=, > and >=. When each vertex element has a user_data element, every attributes in the user_data element can be used to select vertices with equality and inequality operators.

4.2. within expression

A within expression selects vertices that exist within a specified distance from a set of atoms specified by the atom expression.

1) within( <distance>, <atom_expression> )

Instead of a set of atoms, a single point coordinates, from which the distance is measured, can be specified.

2) within( <distance>, [x, y, z] )
3) within( <distance>, {x, y, z} )

In case 2), vertices are selected according to their current coordinates displayed in the screen. On the other hand, coordinates written in the original polygon file are used in case 3).

4.3. box expression

A box expression selects vertices that exist in some cubes, where each cube is centered to each atom in a set of atoms specified by the atom expression. The syntax is similar to that of the within expression.

1) box( <size>, <atom_expression> )

When a single point coordinates is given in the second argument, vertices that exist in a single cube, whose center is set to the passed coordinates, are selected.

2) box( <size>, [x, y, z] )
3) box( <size>, {x, y, z} )

In every cases, the length of an edge of the cubes is twice as the specified value.

5.1. RGB values

A color can be specified by a comma separated triple of Red, Green and Blue (RGB) components enclosed in square brackets, where RGB values are from 0 to 255, respectively.

5.2. Predefined Color

The following 24 colors can be specified by their name.

color name	RGB values	color
BLACK	[0, 0, 0]
BLUE	[0, 0, 255]
BLUETINT	[175, 214, 255]
BROWN	[175, 117, 89]
CYAN	[0, 255, 255]
GOLD	[255, 156, 0]
GREY	[125, 125, 125]
GREEN	[0, 255, 0]
GREENBLUE	[46, 139, 87]
GreenTint	[152, 255, 179]
HOTPINK	[255, 0, 101]
MAGENTA	[255, 0, 255]
ORANGE	[255, 165, 0]
PINK	[255, 101, 117]
PINKTINT	[255, 171, 187]
PURPLE	[160, 32, 240]
RED	[255, 0, 0]
REDORANGE	[255, 69, 0]
SEAGREEN	[0, 250, 109]
SKYBLUE	[58, 144, 255]
VIOLET	[238, 130, 238]
WHITE	[255, 255, 255]
YELLOW	[255, 255, 0]
YELLOWTINT	[246, 246, 117]

5.3. Color Scheme

5.3.1 amino

The color scheme 'amino' colors amino acids as follows.

amino acids	RGB values	color
ASP, GLU	[230,230, 10]
CYS, MET	[230,230, 0]
LYS, ARG	[20, 90,255]
SER, THR	[250,150, 0]
PHE, TYR	[50, 50,170]
ASN, GLN	[0,220,220]
GLY	[235,235,235]
LEU, VAL, ILE	[15,130, 15]
ALA	[200,200,200]
TRP	[180, 90,180]
HIS	[130,130,210]
PRO	[220,150,130]
Others	[190,160,110]

5.3.2 chain

The color scheme 'chain' assigns each macromolecular chain a unique colour.

5.3.3 charge

The color scheme 'charge' colors atoms according to their temperature factor. High values are coloured in blue and lower values coloured in red.

5.3.4 cpk

The color scheme 'cpk' colors atoms according to the element type as follows.

element	RGB values	color
C	[200, 200, 200]
N	[143, 143, 255]
O	[240, 0, 0]
S	[255, 200, 50]
H	[255, 255, 255]
He	[255, 192, 203]
F, Si, Au	[218, 165, 32]
Na	[0, 0, 255]
P, Fe, Ba	[255, 165, 0]
Al, Ca, Ti, Cr, Mn, Ag	[128, 128, 144]
Ni, Cu, Zn, Br	[165, 42, 42]
I	[160, 32, 240]
B, Cl	[0, 255, 0]
Li	[178, 34, 34]
Mg	[34, 139, 34]
Others	[255, 20, 147]

5.3.5 group

The color scheme 'group' colors residues by their position in a macromolecular chain. Each chain is drawn as a smooth spectrum from blue to red. The N terminus of proteins and 5' terminus of nucleic acids are colored red and the C terminus of proteins and 3' terminus of nucleic acids are drawn in blue.

5.3.6 shapely

The color scheme 'shapely' colors residues as follows.

residue	RGB values	color
ALA	[140, 255, 140]
GLY	[255, 255, 255]
LEU	[69, 94, 69]
SER	[255, 112, 66]
VAL	[255, 140, 255]
THR	[184, 76, 0]
LYS	[71, 71, 184]
ASP	[160, 0, 66]
ILE	[0, 76, 0]
ASN	[255, 124, 112]
GLU	[102, 0, 0]
PRO	[82, 82, 82]
ARG	[0, 0, 124]
PHE	[83, 76, 66]
GLN	[255, 76, 76]
TYR	[140, 112, 76]
HIS	[112, 112, 255]
CYS	[255, 255, 112]
MET	[184, 160, 66]
TRP	[79, 70, 0]
A	[160, 160, 255]
C	[255, 140, 75]
G	[255, 112, 112]
T	[160, 255, 160]
Others	[255, 0, 255]

5.3.7 structure

The color scheme 'structure' colors residues according to the secondary structure as follows.

secondary structure	RGB values	color
alpha helix	[255, 0, 128]
beta sheet	[255, 200, 0]
turn	[96, 128, 255]
none	[255, 255, 255]

5.3.8 temperature

The color scheme 'temperature' colors atoms according to their temperature factor. High values are coloured in red and lower values coloured in blue.

5.3.9 type

This color scheme 'type' colors each hydrogen bond according to the distance along a protein chain between hydrogen bond donor and acceptor as follows.

offset	RGB values	color
+2	[255, 255, 255]
+3	[255, 0, 255]
+4	[255, 0, 0]
+5	[255, 165, 0]
-3	[0, 255, 255]
-4	[0, 255, 0]
Others	[255, 255, 0]

6. Command-line Options

When you start up the application from the command-line of your operating system, some options can be passed to the start-up script. For Mac OS X, for example,

startup_macosx.command [options]

The available options are as follows.

parameter	action
-pdbml <file>	opens the PDBML file. Mre than one files, delimited by space, can be spepcified.
-pdb <file>	opens the PDB file. Mre than one files, delimited by space, can be spepcified.
-polygon <file>	opens the polygon file. Mre than one files, delimited by space, can be spepcified.
-animation <file>	opens the animation file. Mre than one files, delimited by space, can be spepcified.
-ftp <pdb_id>	Retrieves the PDBML file from the PDBj FTP site and opens it. Mre than one files, delimited by space, can be spepcified.
-script <file>	opens the script file.
-stdin	listens the stdin stream and receives commands.