GRAPH is a module with prompt: GRAPH>. It is used to displayed text and two dimensional objects (graphs). There are 10 possible GRAPH objects that can be manipulated independently. HIS_RAMA plots the cross of a residue into Ramachandran plot only into object 1. To see the results on the display you must at least once enter the IMAGE DIALOGUE mode.
WARNING: All GRAPH objects are not stored in the program but only transferred to the graphic display. The menu option RE_DRAW will erase them if they are not protected with an IMAGE FROM command. If you want to plot the Ramachandran plot or any other plot, all GRAPH objects must be send to the display when PLOT mode is already ON. When that is not the case, first turn the PLOT mode ON and afterwards repeat the GRAPH commands.
OBJECT inte SCALE real CHARACTER SCALE realEXIT
X-AX real Y-AX real COLOR inte TEXT string TRANSLATION real real real
RAMACHANDRAN
STEP real
ENERGY UNIT inte
SELECT ... END
CROSS
CELL
SEQUENCE
RESIDUE
READ FILE file_name
UNIT int
EXIT returns command input form GRAPH> to MAIN>.
OBJECT inte
OBJECT inte defines the current object and resets the translation of the current objects to default position in
SCALE real
Defines the SCALING of the current OBJECT.
CHARACTER real
Defines the CHARACTER scale of the current OBJECT.
X-AX real Y-AX real Z-AX real
Defines the position for the next TEXT command. It can be changed interactively by using TEXT_TRN mode. The default position is 0.0 0.0 0.0.
COLOR inte
Sets the color that will be used by displaying the following images.
TEXT string
Sends the TEXT to the current position on the screen.
TRANSLATION 3*real
Data used for TRANSLATION of the whole GRAPH OBJECT.
... RAMACHANDRAN STEP real
ENERGY UNIT inte
SELECT ... END CROSS
CELL
SEQUENCE
RESIDUE
Displays Ramachandran plot constituents. STEP draws lines in the frame separated for the real. ENERGY plots the contouring vectors that are read from the file accessible under UNIT inte. CROSS, CELL, RESIDUE and SEQUENCE are used to display a CROSS, squared CELL or RESIDUE name or SEQUENCE name of SELECTED residues at their position in the Ramachandran plot. The SELECT command must precede and not follow the kind of image. Otherwise there may be a mass on the display.
IMPORTANT: dihedral angles PHI and PSI should be present in INTERNAL coordinates data and PAIR list should be created. The required condition,however is, that all the selected atoms are correctly covalently bound. Apply the following series of commands
MAIN> make ztable MAIN> calculate internal MAIN> make pair ramachandran select ... end
and then enter the GRAPH module and prepare the plot. The options ENERGY UNIT and STEP are obsolete now, since any GRAPH can be displayed with the READ FILE command. The RAMACHANDRAN plot background images are made with a READ FILE command sentence now. See Examples.
READ FILE file.name READ UNIT int
READS the graphical commands from the specified FILE or from the FORTRAN logical UNIT number in the the input format for LWPLOT. This is the way to include any 3-D graphs to the display list. Graphs may consist of vector lists, dots and labels. Each GRAPH structure has a name (DISPLY name).
Format
First 6 characters are for the command field (DISPLY, MOVE
coordinates and 16 for the COLOR (2 times 8) hue and saturation. The LABEL text continues from the character number 31 (31 = 6 + 3*8 + 1) to the end of the record. The GRAPH FILE should have the following syntax:...), followed by 24 characters (3 times 8 ) for the X, Y Z
Syntax: DISPLY name COLOR hue saturation MOVE x y z DRAW x y z LABEL x y z THE LABEL TEXT