Sequence Viewer

The Multalign Viewer tool displays individual sequences and multiple sequence alignments. Sequence alignments can be read from external files (several formats) or created by other tools in Chimera. Structures opened in Chimera are automatically associated with sufficiently similar sequences in the alignment. After association,

• mousing over a residue in the sequence shows its structure residue number
• selecting in the sequence selects residues in the structure(s) and vice versa
• structures can be superimposed using the sequence alignment

Various measures of sequence conservation and structural variation (RMSD) can be computed and shown above the sequences as histograms, and on the structures with color or worm radius. Secondary structure elements can be depicted as colored boxes or regions on the alignment. Regions can also be created by hand.

(More features...)

G Protein Interface Surface

Heterotrimeric G protein (Protein Data Bank entry 1gg2) with the alpha subunit shown in green, the beta subunit in light blue, and the gamma subunit in brown. The Intersurf tool was used to show the interface between the alpha and beta subunits. The interface surface is colored to show the distance between atoms across the interface (red for closer together, blue for farther apart). (More samples...)