Multiple Sequence Alignment

Multiple sequence alignment of structure chains in Chimera or realignment of the sequences in an existing alignment can be performed using web services hosted by the UCSF RBVI. The following programs are provided:

• Clustal Omega
• MUSCLE

The result is automatically shown in Multalign Viewer. (Sequences can also be added to an alignment one by one without a web service, but true multiple sequence alignment is often advantageous.) (More features...)

Sliced Potassium Channel

Potassium channel (Protein Data Bank entry 1bl8) on a dark slate blue background with potassium ions shown in firebrick. The channel is comprised of four chains. Each chain has been rainbow-colored from blue at the N-terminus to red at the C-terminus, but only the surface of the channel is shown. The surface has been sliced with a per-model clipping plane. The surface cap color is plum except with opacity set to 0.8. The shininess and brightness have been set to 128 and 8, respectively, and the lights on the scene have been moved from their default positions. The subdivision quality (related to the smoothness of the spherical ions) is 5.0, and the molecular surface was computed with probe radius and vertex density set to 1.0 and 6.0, respectively. (More samples...)