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 ___________________________________________________________ Yahoo! For Good helps you make a difference http://uk.promotions.yahoo.com/forgood/
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#fitmode... 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.htm... 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
Hi Lasanthi,
The fit optimization is very simplistic and does not currently avoid clashes between neighboring molecules.
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?
Take a look at colores in the situs package: http://situs.biomachina.org/ HTH, Sabuj
participants (3)
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Pabhashi Fernando -
Sabuj Pattanayek -
Tom Goddard