[Chimera-users] Fitting multiple pdb models

[Tom Goddard]

Hi Lasanthi,

  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:

    
http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmodel

If you get a Chimera daily build (our most recent code)

    http://www.cgl.ucsf.edu/chimera/alpha-downloads.html

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.

    
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/fitmaps/fitmaps.html

  The fit optimization is very simplistic and does not currently avoid 
clashes between neighboring molecules.

    Tom



Pabhashi Fernando wrote:
> Hi,
>  
> 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,
> Lasanthi