Combining Structure with Other Data

• Structure provides spatial information
• Sequence adds non-spatial information
• "The whole is greater than the sum of the parts"

Demonstration Outline

Basic sequence-structure crosstalk:

• Sequence shows the individual sequences of structure chains
• selecting in sequence selects structure and vice versa
• pastel boxes show helix and strand assignments
• mouse over sequence reports structure residue name/number

Multiple sequence alignment from a file:

• external sources include many other programs and databases; example is from PFAM
• shown with Multalign Viewer (actually same tool as Sequence)
• sequence-structure association is automatic, tolerates some mismatches
• many appearance settings (Multalign Viewer preferences)
• lines of information above the sequences are “headers”
• numerical headers are automatically assigned as residue attributes of associated structures
• many options for calculating Conservation header (Multalign Viewer preferences)

When multiple structures are associated with an alignment:

• structures can be superimposed based on the sequence alignment
• RMSD header shows “spatial conservation”

Creating sequence alignments in Chimera:

• MatchMaker creates pairwise sequence alignments which are then used to superimpose the structures
• given a multiple structure superposition (regardless of how it was made), Match→Align creates a multiple sequence alignment
• sequence alignments can be saved in many formats, those that can be read plus EPS