Graphic Display

ribbons

Run the main graphics program to display any *.model files and associated data in the current directory.

usage:
ribbons [options] 

  options:
    -n ModelName -- load specific model
    -f           -- start in fast-draw mode
    -d           -- use dial box if available
    -h           -- start ribbons-help
    -e file.pdb  -- create default model from PDB entry
    -w ix,iy     -- initial window size in pixels 
                    (!no space by comma)

ribbons-help

Invokes hypertext help screens in World Wide Web HTML format. Also invoked by selecting ``Help'' while running ribbons

usage:
ribbons-help

ribbons-demo

Run the demonstration script --- temporarily places the user in the $RIBBONS_HOME/data directory, then invokes the main program. Can use all the `ribbons' options except `-e'.

usage:
ribbons-demo [options]

ribbons-image

Run the demo image viewing script. Shows sample images and describes the interactive settings and files in the $RIBBONS_HOME/data directory used to create them.

usage:
ribbons-image

ribbons-gallery

Run the image viewing script of interesting images created by ribbon, ribbons and Ribbons++ .

usage:
ribbons-gallery

ipaste

Display a saved image file. This is the standard SGI image viewing tool (for more information: man ipaste ). There are so many useful tools SGI available, eg "imgworks".

usage:
ipaste image-file.rgb [options] 

  options:
    -n      --- display with no border
    -o x y  --- display with origin at screen x,y

ilabel

Add labels to a saved image file. I wrote this using the standard SGI image viewing library. The display is pop-up menu driven (Press RightMouse):

usage:
ilabel input-image.rgb output-image.rgb 

  menu options:
    Color      -- invoke sub-menu to select label color
    Fonts      -- invoke sub-menu to select label font
    Points     -- invoke sub-menu to select label size
    Open Color -- open control panel window to modify colors
    Undo Last  -- erase the last string placed
    Save       -- write the labeled *.rgb file and exit program
    Quit       -- quit the program, without saving file

Arbitrary text is entered at the keyboard until RETURN is pressed. Text is then placed on the image begining at the current cursor position by clicking the LeftMouse button. If there is a problem, select "Undo Last" (Note: this ONLY will undo the very last string entered). Clicking the LeftMouse again after undo will redisplay the last string.

iwhite

Convert the background color of an image to white, eg, convert a slide image to one better for printing.

usage:
iwhite input-image.rgb output-image.rgb

Place cursor over a background pixel, press LeftMouse to save and echo color. Press MiddleMouse to convert each pixel of that color into white. Press RightMouse to save output, press Escape to exit.

rama-plot

Displays a phi/psi plot from the diagnostic output of the "pdb-rama-ss" program.

usage:
rama-plot [options] < pdb-rama-ss.out
pdb-rama-ss mol.pdb mol.ss | rama-plot 

  options:
    -x  ---  label the bad phi/psi values

Clicking a circle with the LeftMouse button will identify the residue. Clicking the MiddleMouse button will clear all labels. For nice PostScript plot, use: rama-ps.

chis-plot

Display small chi1/chi2 plots of each amino acid from the diagnostic output of the "pdb-chi-ss" program.

usage:
chis-plot [options] < pdb-chis-ss.out
pdb-chis-ss mol.pdb mol.ss | chis-plot

Clicking a circle with the LeftMouse button will identify the residue. Clicking the MiddleMouse button will clear all labels. For nice PostScript plot, use: chis-ps.

Ribbons User Manual / UAB-CMC / carson@cmc.uab.edu