From GeneDoc to RasMol? Sound complicated? Perhaps, but its really very easy. Let me show you what I did, just for fun of course.
First off, I needed an alignment. Someone suggested using the Trypsin family of Serine Proteases and seeing if GeneDoc could find some important features of a Trypsin molocule. Since GeneDoc can look for contrasts between Families, looking for features of the Trypsin family as compared to Chymotrypsin and Elastase seemed a logical way to go. As you will see, I was able to use GeneDoc to find the active site, as described in the prosite datafiles, the Specificity site by contrasting with Chymotrypsin and Elastase, and show general Physiochemical properties of the molocule.
The first step was making an alignment. I tried making a few alignments with the standard alignment tools, but the Trypsin family specificity pocket was a tough one to line up. Then I found what I needed in the ALI_3D files I had previously converted from the Argos groups at EMBL. Since these files were aligned for structure, the specificity pockets, as well as everything else, was lined up very nicely.
The original file ALI_3D file was much larger, so I trimmed it down to what I was interested in. The above alignment was the result. I used two of the many original groups, the Trypsin group and the Elastase/Chymotrypsin group.
I used GeneDoc's Search Display mode features to search the prosite.dat file for the Trypsin active sites.
Shown above is one of the active sites found, and the Search Display Mode menu. I'd say this worked out very conviently!
Since the groups were already defined, I set the score table to Blosum 100 and switched to Group Contrast Mode. This brought out two of the three specificity sites in the Trypsin molocule.
Knowing that the active site of the molocule is charged, I thought that thePhysiochemical properties would be useful information as well. You can see one of the active sites has a positive charge in the Physiochemical Display Mode of GeneDoc below.
Now I have all the information I want to put into the RasMol display.
It took a little effort to match the PDB file with my alignment. There are sometimes deletions in the PDB files that are not present in alignments. In most cases I am able to insert a few 'X's at the appropriate locations in the alignment. I did that for this alignment as well. I also did some manual renumbering of the amino's in this PDB file, 2PTN.PDB. I did that because there was numbers such as 188A followed by 188 in the PDB file. It took me about 20 minutes to get the residue locations in the .PDB file to match to my alignment. This was the first time I decided to change a.PDB file, and adjustments to the alignment have been much easier for most other .PDB files.
Then I started making RasMol scripts from GeneDoc. I switched to the Search Display Mode and saved the first script.
The first script shows the active sites in Ball and Stick format. I saved this script as 2ptn-1.scr. Then I switched to the Group Contrast Display mode and saved the second script.
This script shows the Group Contrast shading as spacefilled atoms, I saved it as 2ptn-2.scr. Last, I switch to Physiochemical Display Mode and save the last script.
This script only applies Physiochemical shading. Note, as in the second script, the clear all option has been unchecked. In this last script, no sidechains are displayed, thus having the effect of applying the final coloring to the RasMol display.
Now to load up RasMol, open my 2ptn.pdb file and read in the script files.
And tada, my final image can be saved directly from RasMol ...
In the center you can see the amino acids of the active site in ball and stick format. Part of the specificity pocket shows up in yellow as spacefilled atoms. There are other spacefilled atoms the contrast mode detected, but these are likely 'noise' or unimportant amino acids on the outside of the molocule. You can see that there is no conserved Physiochemical property for these other spacefilled atoms. The Physiochemical shading applied last was not only useful for this, but as well in showing the charged area of the active site, as shown in the blue ball and stick figures of the active site.
The files used to create this image are included here as sprot.zip.