Prime User Manual - ISP

Chapter 2: Using Prime–Structure Prediction
• Residue Type: Each amino acid sequence is colored according to the array of residue type
colors.
• Residue Property: Each amino acid sequence is colored according to the array of residue
property colors (fewer colors than residue type).
• Residue Matching: The query and templates are colored in a pairwise manner. Matching
residues are colored according to their residue type, and nonmatching residues are colored
standard gray. If more than one template is chosen, the query will have more colored
residues because the effect is cumulative. If only the query sequence is shown, it is colored
standard gray for all residues.
• Residue Homology: Aligned query and template residues that are identical (highly conserved)
are colored red. Aligned query and template residues that are similar according to
the BLOSUM62 scoring matrix (conserved) are colored yellow. Gray is used for residues
with no homology.
• Secondary Structure: The query sequence is colored standard gray. All other AA
sequences should have SSAs, which are colored according to the SSA colors.
• Template ID: Only available for the Comparative Modeling path. The query sequence is
colored standard gray. The predicted structure is colored according to template ID for
each region (using the cycle colors). Each template sequence is colored with its color, but
only in the region that was used (the rest of the template is colored dark gray to indicate it
is not used).
• Proximity: At any step in which the sequence viewer is displaying sequences that have
associated structure (all steps except Input Sequence), color by proximity mode is available.
When you select this color scheme, the current sequence colors do not change
immediately. Instead, when the mouse is over a sequence that has structure, the cursor
changes to indicate that proximity can be calculated. You can then select one or more
contiguous residues in the sequence, and the system will color that sequence based on the
proximity to the selected residues. No other sequences will have modified colors (even if
they have structure too and are in proximity of the selected sequence).
Proximity is calculated based on the shortest distance between any two atoms in two residues,
not including the bonded C and N atoms in the residues next to the selected
residues.
To change the proximity cutoff, choose Preferences from the Display menu and change
the number in the Proximity cutoff text box.
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