The IMAGE command sentences INITIALIZE the graphical display and prepare images of atoms, bond, labels, points and maps. The DIALOGUE command word transfers the command input to the interactive devices (DIALS and MOUSE).
Picked atoms are stored in the HISTORY list. Only the atoms included in the KEY "image" are pickable. The key "image" is updated each time when an IMAGE of a SELECTION is created, so that the SELECTION is included into the key "image". The key image can, however, be modified interactively with a KEY command.
First an atom must be picked and afterwards a function on the last picked atom(s) is activated and not reverse. Atoms can be sequentially DROPPED from the HISTORY list. The last picked atom is dropped as the first one. Each command picked from the menu is actually translated into one or more command sentences, that could be in principle also typed in from the keyboard.
SELECT ... END
DIALOG **
GROUP INITIALIZE
ON / OFF
NAME string
INCLUDE int1 int2
REMOVE int1 int2
SHOW
VISIBLE
ATOM NUMBER
NAME / SYMBOL
CROSS
CLASS
BALL integer
BOND [ ]
DISTANCE
STICKS integer
HBOND [ ]
DISTANCE
STICKS integer
PAIR [ ]
DISTANCE
STICKS integer
FORCE real
RESIDUE NUMBER
NAME / SYMBOL
SEQUENCE
POINTS [integer]
SURFACE CONTACT
REENTRANT
ALL
3ANGLES
RIBBONS
VOLUME
POTENTIAL STEP real RANGE real real
( 0.5 )
DENSITY
NUMBER ON / OFF
MARK SELECT .. END
ON
OFF
MAP integer DENSITY real (integer integer integer)
BOX integer integer integer
X-AX
Y-AX
Z-AX
STEREO ON / TRUE
OFF / FALSE
CRYSTAL
SIDE_BY_SIDE
XCENTER-DIFFERENCE integer
ANGLE real
VIEW real SCREEN real CENTER CALCULATE SELECT .... END
ATOM atom-number
COORDINATES 3*real
X-AX real
Y-AX real
RATIO real
SCALE real
TRANSLATE real real real
STEP OVER TRUE
FALSE
CLIP TRUE
FALSE
Z-AX real
UNIT integer SELECT ... END ... (UNIT 6 ) (SELECT ALL END)
HISTORY INITIALIZE
PICK atom-number
ATOM NUMBER ON / TRUE
NAME / SYMBOL OFF / FALSE
RESIDUE NUMBER
NAME / SYMBOL
SEQUENCE
SEGMENT
DISTANCE
ANGLE
DIHEDRAL
INTERNAL
DROP
CONTINUE TRUE / or/ FALSE
NAME TRUE /or/ FALSE
MENU OFF /TRUE
ON /FALSE
PAGE int
ERASE
INITIALIZE
DELETE
FROM (integer)
COLOR integer
SET
PLOTTER (
)
ON
OFF
UNIT
LWPLOT
RASTER3D
INITIALI
XCENTER integer YCENTER integer AXCENTER real AYCENTER real
LIGHT integer ON
OFF
COLOR 3*real
PHI real
PSI real
DISTANCE real
COORDINATES 3*real
ANGLE real
ATTENUATION 2*real
EXPONENT real
AMBIENT
DIRECTIONAL
POSITIONAL
SPOT
SHADOW integer
REFLEX BY integer
NUMBER integer real
... SELECT ... END ...
When a SELECT sentence stands before any other command word except UNIT it overrides the default main SELECTION which selects ALL present atoms. When it stands on some other positions the SELECTION (second selection) applies only to the next command word that chooses an atom or point presentation on image. The two SELECTIONS (main and secondary) are related by the logical .AND. operator. The second image selection is the same as SELECT (main image selection) .and. (second image selection) END.
... PLOTTER (
)
ON
OFF
UNIT
LWPLOT
RASTER3D
INITIALI
Turns ON plotting.
Turns OFF plotting.
It writes the plotter form dependent initialization lines.
... UNIT integer
The UNIT command words is used to define the FORTRAN unit to which the PLOTTER data are sent. The unit remains the same for all following image command sentences until a new unit number is defined via an IMAGE UNIT command sentence.
Turn the PLOT mode ON or OFF. When the PLOTTER is on, all the following image commands will result in image on the screen and its copy on a file assigned to number under UNIT. The resulting file(s), can be converted using LWPLOT to the postscript language, that can be interpreted by post script laser printer or by plotters. The created plot files can be also read again in GRAPH with the READ FILE command. By default the PLOTTER mode is turned OFF.
... OVER TRUE
FALSE
IMAGE OVER TRUE redwaws the entire molecular image. The image objects may get reorganized according to their type, color and their active mode (ecah active object is drawn separately).
... MOUSE ON
OFF
Enables or disables the mouse to mimic dials (yo send motion events).
... HISTORY ...
INITIALIZE
PICK atom-number
DROP
ATOM NUMBER ON / TRUE
NAME / SYMBOL OFF / FALSE
RESIDUE NUMBER
NAME / SYMBOL
SEQUENCE
SEGMENT
NAME TRUE
FALSE
DISTANCE
ANGLE
DIHEDRAL
INTERNAL
CONTINUE TRUE / or/ FALSE
HISTORY list is a list of PICKED atoms. The HISTORY list can be INITIALIZED (the count of history atoms is set to 0). The last PICKED atom can always be DROPPED from the list. Up to 200 atoms can be PICKED.
When an atom is picked its HISTORY label appears on the screen. HISTORY label can be composed from ATOM NUMBER and NAME, RESIDUE NUMBER and NAME, SEGMENT name and SEQUENCE name. Flag for each component can be set separately. The visibility of the HISTORY labels can be controlled with the IMAGE HISTORY NAME TRUE or FALSE command sentence.
! CLASS history label - put it in.
... XCENTER integer
Sets the xcenter of the screen relative to the absolute xcenter(axcenter). The default value is 0.0.
... YCENTER integer
Sets the ycenter of the screen relative to the absolute ycenter(aycenter). The default value is 0.0.
!4 WIND integer integer ! Defines the upper right corner of the screen in screen coordinates. ! The lower left corner has 0, 0 x and y values respectively
... AXCENTER integer
Sets the absolute xcenter value.
... AYCENTER integer
Sets the absolute ycenter value.
... VIEW real
Sets the distance from the viewer to the image center along the Z axes. The default value is 500.0. Check with SHOW VIEW.
... SCREEN real
Sets the distance from the viewer to the screen plane along the Z axes or field of view falue. The default value is system dependent. Check with SHOW SCREEN.
... CENTER
Sets the image center to
... ATOM atom-number
Sets the CENTER to the specified ATOM position.
... SEQUENCE string
Sets the CENTER to the CA atom of the residue with the first found SEQUENCE string. When the residue has no CA atom then the center is set to the position of the first atom in the residue.
If there are several residues with the same SEQUENCE id then the first found is taken. If you want to center on some other residue with the chosen SEQUENCE id then apply
> IMAGE CENTER CALCULATE SELECT ... END
command.
... COORDINATES 3*real
Sets the CENTER to specified COORDINATES.
... CALCULATE SELECT ... END
Sets the IMAGE CENTER to the CALCULATED average of the coordinates of the given SELECTION. The default SELECTION are ALL atoms.
... MATRIX integer Z-AX real X-AX real Y-AX real ...
Sets the specified rotation matrix for orientation of the image around specified axes by angle in degrees. Matrix 1 is the default matrix and is used in image processing. See also SET MATRIX.
... STEREO ON / TRUE
OFF / FALSE
CRYSTAL
SIDE_BY_SIDE
ANGLE real
SHIFTS int int int int int int
Stereo commands manipulate stereo projection parameters, the current mode and switch between stereo and mono modes. Default values are installation dependent.
STEREO item on several pages and keyword touch 's' toggle between stereo ON and OFF.
When stereo is ON the SIDE_BY_SIDE stereo mode splits the screen into left and right viewports. Default stereo angle is adjusted for the relaxed eye (positive angle). For crosseyed stereo set a negative angle value.
Defines the crystal eyes stereo mode.
Turns the stereo projections ON.
Turns the stereo projections OFF. Images will apppear in a single viewport.
ANGLE sets the difference in view angle (image is rotated along y) between the left and right image. For the CRYSTAL eyes stereo the ANGLE difference is actually doubled, since left and right image are rotated into opposite directions. The default value is 3.0 degrees.
The value can be set interactively using the DIAL_VIEW item (page 2) dial set.
... shifts 3 * 2 int
If stereo windows don't overlap well adjust the shifts for each window. Each pair of numbers shifts a window for a certain number of pixels in X and Y. The first pair is for the 3-D IMAGE window, the second for the menus on the side and the third for the dials window. the shifts must be specified before you turn the stereo on. Set the stereo angle to 0.0 and start typing shifts. (Don't use glasses when doing it.) When the two images almost ideally overlap you have done it.
It is a bit anoying, but once you have the parameters insert the command into the .main file (after an image init command).
> image stereo shifts 0 0 0 0 0 0
is the default.
... CLIP TRUE / ON
FALSE / OFF
Z-AXIS real
When the automatic clipping is ON (set TRUE) then the clipping planes are defined automatically so that the complete IMAGE appears on the screen. The option shouldn't be applied for larger molecules since it slows down the DIAL respond, However, the IMAGE is displayed with optimal depth contrast. The default flag is set to OFF and the default Z-AXIS value is set to 20.0.
... SCALE real
SCALE defines a scaling factor for the image objects. The image scaling factor should be positive.
... CONTRAST real
Specifies the contrast between front and back of an image. Interval is between 0 and 1.0. 1.0 means no contrast depth (depth cueing off). The default number is hardware and system version dependent.
... RATIO real
Sets the scaling factor for ATOM CROSSES.
... ERASE string
ERASES the screen and clears the programs memory from saved images. The default argument is *, which means that all displayed objects will be ERASED. When image object is explicitly defined only the image labeled with the string is deleted. See also IMAGE FROM.
... FROM integer
Protects displayed IMAGES from erasure. The images bellow the integer number can not be deleted with command IMAGE ERASE. When no image object number is specified, as the default value the last image object is taken.
... INITIALIZE
INITIALIZES the graphic device and established connections.
!WINDOW !Draws the window borders in specified COLOR.
... COLOR integer
Sets the current COLOR for drawing objects on the screen. See IMAGE SET.
... SET
Disables the current COLOR set by the last COLOR command. The program takes the atomic SET colors as specified in module SET_COLOR.
... LINE integer
Defines the line type to be used when drawing vectors. Default is continues line. It doesn't work on PS330.
... DELETE ...
When the DELETE flag is set, the following IMAGE commands do exactly opposite from the usual IMAGE command sentence. The images of selected atoms are deleted from the program's memory and cannot be redrawn any more.
... DIALOGUE (real)
Transfers the control from terminals keyboard to the DIALS and mouse. A specified real number changes the current DIAL scaling factor by multipling it.
... FORWARD
Transfers the control from command line mode (keyboard) to DIALS and a mouse. The difference between this and the DIALOGUE command is that this one changes the mode also when issued in a command file, whereas the DIALOGUE command has no effect.
... BONDS [LINES]
HBONDS DISTANCES
PAIRS STICKS integer
When in COLOR mode is on, all connections between atoms appear in one color, while when the SET mode is on, each connection is divided in 2 parts of equal length, colored according to part's atom color. DISTANCE displays distances of the selected connections. Connections can be displayed also as STICKS (cylinders) with the specified RADIUS and DENSITY of polygons. See SET STICKS ... An integer that can be specified after command word STICKS is a flag that tells whether the polygons are shaded smoothly (more than 0 ) or not ( less or equal 0).
... ATOM NUMBER
NAME / SYMBOL
CROSS
CLASS
BALL integer
ATOM NUMBERS and NAMES / SYMBOLS can be drawn near the selected atom center. CROSS is drawn through the atomic center. The length of cross lines is specified by the RATIO. CLASS displays atom classes or atom types as specified by an SET CLASS or DEFINE command sentence. It is useful for identifying atom types when building a new residue into topology libraries. ATOM BALLS (spheres) are drawn with the currently valid REFLECTION properties and chosen BALL definition (see SET BALL).
... FORCE real
Draws FORCES acting on atoms as calculated by the last ENERGY or MINIMIZE command sentence. The FORCE IMAGE is a vector with origin at the atom center and is pointing (pushing) the atoms in the direction of the gradient. (Pushing with the positive scaling value and pulling with a negative one.) The FORCE unit is kcal/A. When FORCE scaling factor is 1.0 then is the length of the 1 kcal/Amol force 1A.
... RESIDUE NUMBER
NAME / SYMBOL
RESIDUE NUMBER and NAMES or SYMBOLS of selected atoms are displayed.
... SEQUENCE
SEQUENCE symbols can be drawn on the place of residue numbers.
SEGMENT NUMBER
NAME / SYMBOL
SEGMENT NUMBER and NAMES or SYMBOLS of selected atoms are displayed.
... MARK SELECT ... END
ON
OFF
MARKS selected atoms with a star. It is usually activated automatically when KEYS active, passive, image and anchor are being modified from the SELECTIONS menus. The MARKS can be turned ON or OFF.
... POINTS [integer] ...
Since each POINT is related to an atom, they can be also SELECTED with a SELECT ... END sentence. The integer following POINTS is optional. Since on Silicon Graphics machines size of points is not directly adjustable, increasing level from 0 to 1 creates larger spots on screen and slows down dial respond substantially. 1 is recommended to be used for preparing slides.
... SURFACE REENTRANT
CONTACT
ACCESSIBLE
ALL
Points of REENTRANT, CONTACT or both SURFACES (ALL) are drawn. Colors are taken from the atom_color array (the SET mode) or are defined by the color command.
... VOLUME ATOM
ACCESSIBLE
The use of volume points is now obsolete, because their function is more than replaced with operations on the MAP(s).
... NUMBER ON / TRUE
OFF / FALSE
The NUMBER flag can be set ON or OFF. When it is on, the value at a point will be displayed as well. The point values can be either SURFACE, DENSITY, POTENTIAL or VOLUME.
... POTENTIAL STEP real
RANGE real real
When a POTENTIAL or DENSITY points are selected, then the colors of points will be chosen + and - from the defined color for STEP value. Each STEP the color is increased or decreased by 1. When RANGE is specified then only the points in the range will be colored in specified color and drawn. SET flag for atom coloring is meaningless when STEP or RANGE are activated.
... DENSITY STEP real
RANGE real real
When a POTENTIAL or DENSITY points are selected, then the colors of points will be chosen + and - from the defined color for STEP value. Each STEP the color is increased or decreased by 1. When RANGE is specified then only the points in the range will be colored in specified color and drawn. SET flag for atom coloring is meaningless when STEP or RANGE are activated.
... RIBBON LINES
STICKS
RGB
COLOR
Displays ribbons as LINES or STICKS of corresponding color or atom color definition.
See also "SET RIBBON" comamnd in (MAIN_COM:set.html)
... 3ANGLE LINES
AREA
RGB
NORMAL
INVERT
Displays surfaces with filled surfaces eitheras in a single color or corresponding atom color definition.
When RGB each triangle may get variable color, which is interpolated between the colors of each triangle point according to the distance.
NORMAL may be also INCERTED - which enables to look at the surface from its inside.
... MAP intg DENSITY /CONTOUR real (integer_x integer_y integer_z)
BOX / GRIDS integer_x integer_y integer_z
ON
OFF
INCLUDE (int)
REMOVE
X-AXIS
Y-AXIS
Z-AXIS
AREA ON
OFF
LINES
STICKS ON
OFF
DENSITY int
RADIUS real
MAP IMAGE command control displaying of maps. SHOW MAP reveals some map details.
... DENSITY real
Displays the specified MAP at a certain density level.
CONTOUR is a synonym.
... CONTOUR real
Displays the specified MAP at a certain density level.
... BOX integer_x integer_y integer_z
... GRIDS integer_x integer_y integer_z
Turns map redrawal (recontouring) on, so that a RE_MAP will recontour the map at the current center of the screen. This is the default, but you can turn a map recontouring also OFF.
Turns map redrawal (recontouring) OFF, so that a RE_MAP command will not recontour the map at the current center of the screen.
... (int)
You can INCLUDE or REMOVE a map from the display list of image of objects and teher by from the screen. By default a map image is part of the background image (number 0). You can insert it into some other image object and so move the map on the screen as a part of movement attached to atoms (rotations, translations etc...).
Maps whicch are parts of the image displayed on a screen can be REMOVED from the displayed list and later on INCLUDED as well. A shortcut is to press keys from '1' to '0' and maps will be included and removed from the display.
Maps can be contoured as lines along a certain axis (X-AXIS, Y-AXIS, Z-AXIS) or with all three projections simultaneously (LINES) with STICKS ON or OFF.
Maps can be contoured as lines along a certain axis (X-AXIS, Y-AXIS, Z-AXIS) or with all three projections simultaneously (LINES) with STICKS ON or OFF.
Maps can be contoured as lines along a certain axis (X-AXIS, Y-AXIS, Z-AXIS) or with all three projections simultaneously (LINES) with STICKS ON or OFF.
Turns STICKS and AREAS presentation of maps off and turns the default LINES (wire) presentations.
... STICKS ON
OFF
DENSITY int
RADIUS real
Maps contours can be displayed as STICKS (when turned ON) of various precesion (DENSITY) and RADIUS (thickness).
... AREA ON
OFF
Displays MAP as a solid polygonal surface when turned ON.
MAIN> image select pep end bond select atom name CA end - MAIN> residue name
Displays bonds of the key "pep" and at positions of each CA included in the key "pep" also its residue name
MAIN> image color 60 map 3 dens 0.9 5 5 5
Displays in color 60 map number 3 at density level 0.9 in a box 5 grids in all directions from the center.
The DIALOG mode can be entered only from MAIN> directly and not from a command file. The IMAGE and ATOMIC transformations can be driven by dials and commands picked from menus combined with picked atoms in the HISTORY list.
Menu commands are actually shortened notations for command sentences. Some of resulting command sentences appearing in manual within square brackets [] are written by the program and later on executed. Command interpreter does not distinguish between the sentences typed in from the keyboard and the ones written by the program. The command sentences written by the program itself are also stored into the file INPUT.COP before they are executed. So even if no update of coordinates in a file has been done between the run, all the changes off structural data could be retrieved afterwards. In the case of computer or program crash or a mistake the user's effort is not lost as long data from the file are accessible.