Files for a default ball-n-stick drawing were generated:
atom-model his.pdb
The model name 'his' is taken by default from the name of the *.pdb file. The ribbons database for this display is generated by 'atom-model'. Below explains what is going on and the actual ribbons commands issued.
A set of spheres color-coded by atom type was generated:
pdb-atom-sph his.pdb his.sph
A set of split bonds colored by atom type was generated:
sph-bond his.sph his.cyl
The *.atoms file consists of only one filename:
ls his.sph > his.atoms
The *.bonds file consists of only one filename:
ls his.cyl > his.bonds
The *.model file was generated:
pdb-model his.pdb his.model
The data base was enhanced by hand editing 'his.model' file
to change the descriptive name to 'histidine'.
The file 'his.str' was created with the editor to display a single string.
(The string files have the same format as the *.sph files).
The color index is 14 (gold).
The *.texts file consists of only one filename:
ls his.str > his.texts
The model is now ready for display:
ribbons -n his
The window size was maximized before saving the file 'save.rgb'
through the File Menu and PrintScreen.
On my machine, this gives an image 1224x978 pixels.
(Use SGI command 'istat save.rgb' to get pixel size.)
On my machine, the monitor is 1280x1024 pixels.
To make the image as large as possible, use the SGI command:
izoom save.rgb full.rgb 1.046 1.047'
( 1.046 = 1280/1224; 1.047 = 1024/978 ).
The two images were compositied using the standard SGI image tools.
Clip the full screen images in half in X:
subimg full.rgb half.rgb 320 959 0 1023
These two ``half'' images were placed side by side:
ipaste ball.hrgb -n -o 0 0
ipaste stick.hrgb -n -o 640 0
scrsave temp.rgb
izoom temp.rgb his.rgb 0.5 0.5
Note: The 'tobw' command will convert full-color RGB to black and white:
tobw color.rgb bw.rgb
Note: The SGI 'imgworks' command will start a program to do all sorts of image manipulations.