It was made by the following steps.
Go to a directory containing your protein Type:
and
Type: "your PDB filename"
The image on the left was made using neon with a depth cue intensity by changing the following line in the neon.dat file being used (click on "neon" below for more information).
1 0.10 |Depthcue,Fraction |0=n, 1=y; percent aft intensity
This makes the "aft intensity" a tenth of the foreground, causing the tyrosine inside the pocket to appear darker and farther away, without having to have a stereo image. This allows for the overall comparison of the two proteins to be shown on the right, also using neon. The image on the right, on the black background, was created separately, and scaled to be the right size with the SGI utility program "izoom". It was then pasted onto the full image of the active site, where the coordinates were displayed on the left hand side of the screen, using the SGI utility program "ipaste -n filename".
The entire screen was then saved using the "scrsave" command.
More detailed information on one of the commands mentioned here is available by clicking on the following:
Under Construction
setup midas
or
source /sgi/local/bin/midas.set
midas
Last Modified: Wednesday, 21-Aug-2002 12:49:49 EDT