Fitting in EM map with MultiFit and Chimera

Keren Lasker
Tom Goddard
February 23, 2009

Illustration of fitting atomic models into EM map using MultiFit from Sali lab in combination with Chimera.

• Graph calculated for map using k-means, one node per protein.
• Proteins hand placed at presumed locations.
• Optimize placements using MultiFit, handles steric clashes.

Other cases allow specifying restraints for which proteins contact which others and for allowing MultiFit to determine best protein locations on graph.

4 protein nuclear pore targeting complex (simulated map 9 A from 1z5s).	Graph partition of map using k-means algorithm.	Crystal structures for fitting into map.
Hand-placed proteins are associated with closest graph nodes.	Computational optimization by MultiFit program.