Example of thick bond model with selected electron density in stereo

• Load the entire molecule and display a zone (called pep)with white carbons:

sam_at_in prot.pdb

Sam> O associated molecule name: pep

mol pep
obj pep
centre_atom 156
paint_prop atom_name = c* white
z 154 158 end

• Read the small (0.2) cpk radii file to cap the stick bonds (if you want thin bonds read radii_small.o for 0.08):

read radii.o

• Draw the cpk atoms:

sketch_cpk pep

• Set the bond thickness and complexity:

sketch_set

Sketch> Setup for what type? [stick]:
Sketch> Solid, line or smooth mode? [smooth]:
Sketch> Radius? [ 0.2]:
Sketch> Number of edges [ 4]: 10

• Draw the bond cylinders:

sketch_stick pep

• Draw map around zoned residues (parameter the map any size and then reduce it by the map_cover command):

map_file map.dn6
map_active_centre
map_obj map
map_par 10 10 10 1. lime_green 0.5 0.1 1
map_cover pep 1
map_dr

• Hit F3 to enable hidden lines.

• Adjust the view with SLAB and ZTRANS dials. When you are happy with the settings save the current view matrix:

write .gs_real matrixpep.o ;

Every time you read in this matrix it restores this view, i.e.

read matrixpep.o

• Size the window and launch snapshot or import (DEC's). Hit F2 to hide the menus.

• Rotate the picture by three degress to the left and take the right-eye picture:

rot_pic y -3

• Snap it.

• Rotate the picture by 6 degrees to the right and take the left-eye picture:

rot_pic y 6

• Snap it.

• Convert the files to TIF format using XV or convert and transfer to a PC/MAC running canvas.
• Launch canvas. Set the ruler to cm Layout>Rulers choose ruler 3, set spacings to 10. Show rulers and grids Layout display. For 1/2 shots on the fuji adjust your document size to 22 cm wide 15 cm high. Load the images File>Place set the density in the popup to 400 dpi (works good for the Fuji, depends on the output device). Don't worry if they look crummy, Canvas only displays a proxy to speed up display. Adjust the images so they are ~6.5 cm apart. Select the Selection Tool and double click on the on image. Adjust the color intensity Image>Adjust>Curves? Select RGB channel and drag the center point all the way up so that the input is 125 and the output 255. Repeat the process with the other image.
• Stereo labels: The stereo separation is actually encoded in the position of the atoms. All you have to do is place identical labels on identical ATOMS i.e. OH of a Tyr residue, (3.5-5 points size depending on the depth), group these 2 labels (Control G). Now move them around where you want them. The separation of these labels determines their depth position.
• Save the file as TIF with 400 dpi, transfer and print. On the Fuji no color correction is necessary, may be a slight reduction in brigthness.

Last Modified: Monday, 14-Dec-1998 16:25:28 EST