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 -- initial window width in pixels (5/4 aspect maintained)
-V output.pov -- create POV files from input and exit
-W output.pov -- create VRML files from input and exit
-S disulphides.cyl -- create disulphide *.cyl files and exit
-B c_beta.cyl -- create ribbon-CB *.cyl files and exit
-A base_attach.cyl -- create base attachment *.cyl files and exit
-H base_hbond.cyl -- create base H-bond *.cyl files and exit
(sorry, -I temporarily disabled. will have to save interactively)
-I image.tiff -- create TIFF image file from input and exit
usage:
usage:
usage:
usage:
usage:
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.
usage:
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.
usage:
usage:
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.
ribbons-help
Invokes hypertext help screens in World Wide Web HTML format.
Also invoked by selecting ''Help'' while running ribbons
ribbons-help
ribbons-demo
Run the demonstration script --- temporarily places the user in the
$RIBBONS_HOME/data directory, then invokes the main program.
Select from 'Model' on the menubar to see an example.
Can use all the 'ribbons' options except '-e'.
ribbons-demo [options]
ribbons-image
Browse sample images and descriptions of the interactive settings
and files in the $RIBBONS_HOME/data directory used to create them.
ribbons-image
ribbons-gallery
Browse various interesting and historic images created
by ribbon, ribbons and Ribbons++ .
ribbons-gallery
rama-plot
Displays a phi/psi plot from the diagnostic output
of the "pdb-rama-ss" program.
rama-plot [options] < pdb-rama-ss.out
pdb-rama-ss mol.pdb mol.ss | rama-plot
options:
-x --- label the bad phi/psi values
chis-plot
Display small chi1/chi2 plots of each amino acid
from the diagnostic output of the
"pdb-chi-ss" program.
chis-plot [options] < pdb-chi-ss.out
pdb-chi-ss mol.pdb mol.ss | chis-plot
ipaste
SGI only.
Display a saved *.rgb image file with the standard SGI
image viewing tool (for more information: man ipaste ).
There are so many useful tools SGI available,
eg, 'imgworks', 'imgcopy'...
ipaste image-file.rgb [options]
options:
-n --- display with no border
-o x y --- display with origin at screen x,y
ilabel
SGI only.
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):
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