As you walk through this tutorial, notice many of the new images you've
created in the OpenGL Display. Often these images are generated by highlighting
specific portions of the aligned protein sequences. If you would like to
study your selections further, you can can do so by generating your own PDB
file(s). To begin this process:
1
Highlight the portions of the sequence that you want to examine in the
Sequence Display of the main Multiple Alignment window.
2
In the main Multiple Alignment window top pull-down menu, go to View Highlight
style.
Multiple Highlight styles will appear to choose from. Select one and make sure it appears in the OpenGL Display.
3
Go back to the Multiple Alignment window and click on File Write PDB from
selection....
4
The PDB file(s) will be saved in a directory that can be chosen by clicking on the File Choose
Work Directory.... If you haven't selected your Work directory, you be prompted to choose a directory when you click on
Write PDB from selection....
5
If you want to save the entire alignment, you can do so by going the Residue Selection and selecting Q Value, Greater than, and 0.0. Then click on the Select button in the Q Value window. The four
sets of sequences will be highlighted. Go to File Write PDB from selection... and four PDB files will be generated.
Figure 24:
Where the generated PDB files will appear.