Select Residues

The Residue Selection feature (See Fig. 10)lets you analyze conservation using different measures, and highlight residues in the Sequence Display and VMD OpenGL Display simultaneously. Residue Selection allows you to examine the conservation on a per residue basis.

Figure 10: Select Residues Window

There are two options: either Where Sequence Identity is or Where $Q_{res}$ is. Where Sequence Identity is is a sequence identity measure, whereas Where $Q_{res}$ is is a structure measure( For more on $Q_{res}$ see 10.3).

Select residues in:

You can choose all sequences or just the marked ones.

Where Sequence Identity is:

If this option is selected you can select `less than or equal to' or `greater than or equal to' option, then a number between 0-99%.

Where $Q_{res}$ is:

If this option is selected you can select `less than or equal to' or `greater than or equal to' option, then a number between zero and one.