Example of thick bond model with selected electron density in stereo
(Thanks to Carsten Schubert for working this out the first time).
- Load the entire molecule and display a zone (called pep)with white carbons:
Sam> O associated molecule name: pep
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):
- Set the bond thickness and complexity:
Sketch> Setup for what type? [stick]:
Sketch> Solid, line or smooth mode? [smooth]:
Sketch> Radius? [ 0.2]:
Sketch> Number of edges [ 4]: 10
- Draw map around zoned residues (parameter the map any size and then reduce it by the map_cover command):
map_par 10 10 10 1. lime_green 0.5 0.1 1
map_cover pep 1
- 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.
- 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
- Rotate the picture by 6 degrees to the right and take the left-eye picture:
rot_pic y 6
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