[Chimera-users] Fitting multiple pdb models
goddard at cgl.ucsf.edu
Mon Apr 7 12:03:10 PDT 2008
You can place molecule models in EM maps by hand in Chimera and you
can locally optimize their position and orientation (steepest descent
optimization) with the "Fit in Map" tool. Here's how:
If you get a Chimera daily build (our most recent code)
the Fit in Map tool can produce a simulated map at the desired
resolution and report a correlation coefficient that measures how well
each molecule fits into the map.
The fit optimization is very simplistic and does not currently avoid
clashes between neighboring molecules.
Pabhashi Fernando wrote:
> I am at the moment trying Chimera, and quite like it!
> This is to get a clarification: I need to fit 6 independent pdb models
> that account for different domains of the protein into my EM map. How
> can I do this? And, is there an evaluation criterion for the fitting?
> Many thanks.
> Best wishes,
More information about the Chimera-users