The SHOW command sentence is to be used for interactive control of data (ATOM, BOND, RESIDUE, SEGMENT, SELECTION number, IMAGE parameters ...) and for some data analyses and statistics. Each of the SHOW command group can be continued within the same command sentence by starting a new command group at the end of the previous. Most of the parameters that can be SET can be also SHOWN.
FILE stringUNIT int
IMAGE
ALL
AUTO_DIA
BALL
CENTER
CLIPPING
COLOR
CONTRAST
DIALS
FONT
HISTORY
LIGHTS
LIST
MATRIX
RATIO
REFLECTI
SCALE
SCREEN
STEREO
STICK
TRANSLAT
VIEW_CEN
WINDOW
BOX SELECT ... END
BOND
ATOM
RESIDUE
SEGMENT
SIZES
PLANE LIST
ANGLE int int
DISTANCE atom-num int
POINTS SURFACE ALL RESIDUE
CONTACT RANGE real real
REENTRANT STEP real
ACCESSIBLE
VOLUME ALL
ATOM
ACCESSIBLE
DENSITY
POTENTIAL
TEXT
MATRIX
KEY / SELECTION
VARIABLES
TOPOLOGY LIST
RESIDUE string
ATOM string CHARGE CLASS / ALL
INTERNAL_COORDINATES
ZTABLE_CONNECTIONS
VARIABLE_NAMES
GROUP_NUMBER
BOND
DIHEDRAL
IMPROPER
PARAMETERS BOND string
ANGLE string
DIHEDRAL string
IMPROPER string
VdW string
ENERGY
FORCES SELECT ... END
DENSITY SELECT ... END
RESIDUE
OBJECTS
COLOR SELECT ... END
RADII SELECT ... END
CHARGE SELECT ... END
CLASS SELECT ... END
WEIGHT SELECT ... END
TEMPERATURE SELECT ... END
RESIDUE
LIST
STEP
RANGE
DISTANCE atom-num atom-num
ANGLE atom-num atom-num atom-num
DIHEDRAL atom-num atom-num atom-num atom-num
INTERNAL atom-num atom-num atom-num atom-num
... UNIT int
Redirects the SHOW output to the logical UNIT number int.
... FILE string
Redirects the SHOW output to the specified FILE.
... ALL
(
)
AUTO_DIA
BALL
CENTER
CLIPPING
COLOR
CONTRAST
DIALS
FONT
HISTORY
LIGHTS
LIST
MATRIX
RATIO
REFLECTI
SCALE
SCREEN
STEREO
STICK
TRANSLAT
VIEW_CEN
WINDOW
Shows image parameters. ALL shows all of them, whereas use of "( ... )" enables you to specify a list.
Automatic generation of dial events.
The shown parameters are the current plygonal approximations applied for ATOM BALL generation.
Use "POINT BALL" commands to modify them.
Shows the current image CENTER in X, Y, Z.
Use "IMAGE CENTER" commands or dials to change it.
Shows the current clipping planes.
Shows image contrast value.
Shows HISTORY display label flags and, when requested, the list of picked atoms.
Use "IMAGE HISTORY" commands or pick the atoms using a mouse to create the list and edit it (menu block "HISTORY"), and menu block "HISTORY_FLAGS" to change the label definitions.
Shows current light sources status and parameters.
Use "IMAGE LIGHT" commands and SET DIAL nn LIGHT commands together with dials to modify them.
Lists all deposited image objects, their on / off status and color.
Shows the current view matrix.
Use dials and "IMAGE MATRIX" commands to modify it.
Shows ratio number. The number is used ofr control the size of ATOM CROSSES etc...
Use "IMAGE RATIO" commands to spefify it. Default is 0.2.
Shows reflectance coefficients.
Scale of image,
SCREEN to eye (viewwer) distance.
Stereo projection parameters, mode and status.
Shows parameters applied for BOND STICK generation.
Use SET STICK commands to define them.
The current translation of the image, apart from the center of rotation.
Use "IMAGE TRANSLATE" commands to change the translation.
Shows viewer to center of the obect distance.
Shows the current size of image window in pixels.
... ATOMS
SHOWS the number of present ATOMS.
... BOX SELECT ... END
SHOWS the BOX limits of the SELECTED atomic coordinates.
... RESIDUE
SHOWS the number of present RESIDUES.
... SEGMENT
SHOWS the number of present SEGMENTS and lists their names and counts the atoms inside each one.
Shows sizes of most important data arrays (atoms, points, refelctions, maps).
... PLANE LIST
ANGLE int int
DISTANCE atom-num int
LISTS currently present planes with their PLANE equations, SHOWS ANGLE between the two specified planes and the DISTANCE of an atom from the plane (int denotes the PLANE number and atom-num an ATOM NUMBER).
... POINTS (SELECT ... END)
SURFACE ALL RESIDUE
CONTACT RANGE real real
REENTRANT STEP real
ACCESSIBLE
VOLUME ALL
ATOM
ACCESSIBLE
DENSITY
POTENTIAL
Each point belongs to an atom, so that SELECT statement can be applied. The default SELECTION are ALL atoms.
The 4 kinds of points (SURFACE, VOLUME, map DENSITY, electrostatic POTENTIAL) can be checked and some statistics can be done with their values. The SURFACE points are divided also further in CONTACT, REENTRANT, ACCESSIBLE points and VOLUME points into ATOM and ACCESSIBLE points.
When nothing else is required only the range, sum, average value per point and number of SELECTED atom points are displayed. With RESIDUE, the same data are displayed for each RESIDUE separately and per an averaged ATOM in the residue. With RANGE the points with their values in the specified RANGE are counted. When the STEP is defined, then they are counted for each STEP interval in the specified RANGE.
... MATRIX
Shows all (8) 3*3 MATRICES used for rotation transformations.
... KEY / SELECTION
Displays the list of KEYED SELECTIONS with the number of atoms included in each one.
... KEY / SELECTION
Displays the list of KEYED SELECTIONS with the number of atoms included in each one.
... CHAIN SELECT ... END
Shows a summary of residue and atom numbers included in each chain.
... VARIABLES string []
NUMBER
Displays the list of to the 'string' matching integer, real and character VARIABLES with their values. With no further argument the usual long description is used. With the NUMBER only the variable values without variable names are SHOWN.
... TOPOLOGY LIST
RESIDUE string1
ATOM string2 []
CHARGE
CLASS
COORDINATES
ALL
INTERNAL string2
ZTABLE string2
VARIABLE string2
GROUP string2
BOND string2
DIHEDRAL string2
IMPROPER string2
The SHOW TOPOLOGY gives insight into the TOPOLOGY library. With LIST all present RESIDUE names can be listed. With the RESIDUE 'string', only the matching residues are listed. To get the list of ATOMS, INTERNAL coordinates, ZTABLE, BONDS, DIHEDRAL and IMPROPER angles ... of the chosen 'string2' atoms. The ATOM list, can include besides the atom names (without a further argument), also partial atomic CHARGES, atom CLASSES and initial COORDINATES. ALL lists CHARGES, CLASSES and COORDINATES.
... PARAMETERS BOND string
ANGLE string
DIHEDRAL string
IMPROPER string
! VdW string
The SHOW PARAMETER ... lists all force field parameters including the particular atom CLASS.
... ENERGY
Displays the currently turned on ENERGY terms with the last calculated ENERGIES.
... FORCES SELECT ... END
SHOWS the list of last calculated forces acting on the SELECTED atoms.
... DENSITY SELECT ... END
RESIDUES
Calculates the DENSITY energy of the SELECTION. With RESIDUES, it prepares a list of the density energy for each SELECTED RESIDUE and calculates an averaged atom contribution to it. With different weighting factors and density energy options several lists can be prepared (see MAIN$EXA:[DENSITY]).
... OBJECTS
Shows the list of the current active OBJECTS with their definitions and their values.
... COLOR SELECT ... END
Lists COLORS of the SELECTED atoms.
... CHARGE SELECT ... END
Lists partial atomic CHARGES of the SELECTED atoms.
... CLASS SELECT ... END
Lists CLASS of the SELECTED atoms.
... RADII SELECT ... END
Lists atomic RADII of the SELECTED atoms.
... WEIGHT SELECT ... END
Lists crystallographic WEIGHTS of the SELECTED atoms.
... TEMPERATURE SELECT ... END []
LIST
RESIDUE
RANGE real real
STEP real
With no argument [] calculates the average TEMPERATURE factor of the SELECTION. With the LIST writes the list of temperature factors. Per RESIDUE calculates average temperature factor for each RESIDUE and with the RANGE and STEPS it counts all atoms that are in the specified RANGE for each STEP size separately.
... DISTANCE 2*atom-num
SHOWS the DISTANCE between the 2 atoms in Angstroems.
... ANGLE 3*atom-num
SHOWS the ANGLE defined by the 3 specified atoms in degrees.
... DIHEDRAL 4*atom-num
SHOWS the DIHEDRAL angle defined by the 4 atoms in degrees.
... INTERNAL 4*atom-num
SHOWS INTERNAL coordinates as defined by the 4 atoms (DISTANCE, ANGLE and DIHEDRAL angle).
MAIN> show image all MAIN> show bond MAIN> show color select symbol atom C* .and. number residue 1 5 end MAIN> show topology residue GL%% atom C* internal ztable MAIN> show internal 3 4 100 6789 MAIN> show keys