|List of Images|
JPEG version (64KB), TIFF version (835KB)
This image shows two different substrates as they bind in the active site of the HIV-1 protease. On the left, neon was used to display the substrates. On the right, conic was used. In order to get a transparent ghost of where the green substrate fits inside the magenta substrate space, two images were made and blended together.
The first image had a side by side image using neon and conic. The preneon command allows you to make a file that has the atomic coordinates for both a stick and a sphere image in the same file. The file is quite large, however, and should be removed when you are through making it.
First get the substrates as you like them on the full screen. Make it so that the image you desire only fills up the left half of the screen.
Save these coordinates into a file.command: pdbrun cat > coords.file
Open these coordinates as a second model. Then, move them to the right side of the screen. You should now have identical coordinates on the screen, even if the one on the right is not connected properly anymore.
Now undisplay the new set of coordinates and do a "preneon" to get the coordinates on the left to appear in neon format.command: ~display #2 (or whatever the new model number is of the newly opened coords.file) command: preneon cat > balls_and_sticks.file
Now get the coordinates on the right for use as normal full size spheres.command: ~display command: display #2 command: preneon cat >> balls_and_sticks.file DON'T FORGET TO USE TWO ">" SIGNS. This causes the stick coordinates to be added to the balls_and_sticks.file, rather than writing over the work you have already done.
Finally, make a conic picture that only has the green substrate in it. This will end up being the strongest color in the image.command: ~display command: display #2:sub (where "sub" is the name of the residue) command: conic -o substrate.pic
After getting out of MidasPlus, render the file "balls_and_sticks.file" using the Conic delegate program.conic -o all.pic balls_and_sticks.file "all.pic" is the name given to a picture containing all the elements, both neon and conic renderings, of the inhibitors.
You are now left with to images having the ".pic" ending, as you named them; all.pic and substrate.pic. The SGI utility program "blend" can be used to combine these two images into a semi-transparent looking image.blend all.pic substrate.pic final.pic .5
View your results using the "imgview" SGI utility program. The "-n" stands for "no border". Quit this image using the "alt" key and the right mouse.imgview -n final.pic
©2004 The Regents, University of California; all rights reserved.