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.

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Thermosome

Thermosomes are hollow balls inside which proteins are folded. They are found in the cytosol of eukaryotes and in archaea. Eukaryotic thermosomes have 8 different protein subunits, while archaeal ones are composed of one, two or three different proteins. The one shown from Thermoplasma acidophilum has two distinct proteins colored blue and yellow, each present in 8 copies. The two proteins have 60% sequence identity and are very similar in structure. One monomer is shown as a ribbon. Actin and tubulin are folded by eukaryotic thermosomes.

Protein Data Bank model 1a6d.

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