[Chimera-users] fit molecule with Laplacian filtered map
goddard at sonic.net
Wed Aug 31 20:17:56 PDT 2011
The Laplacian filter is a second derivative filter and it is normal
that it gives positive and negative values -- basically doing edge
detection. You would only use that with Chimera fitting routines to fit
one Laplacian filtered map into another Laplacian filtered map. I have
no experience whether that is a useful technique. I have heard it can
be used to match boundaries. It is not a routine fitting approach and
you'll need to do extra work to use it and it may not work well at all.
So be careful.
> This is my first time trying to apply the Laplacian filter to a
> cryo-EM map in Chimera before I perform the global search to fit my
> crystal structure. However, the resulting map looks like the original
> map blown up into million pieces with positive and negative density
> showing. I get the same effect even after I "smooth" the map with the
> Gaussian filter first.
> Could someone advise me on how I could use this Laplacian filtered map
> information to better fit my molecule into the original EM map?
> Thanks for your help in advance.
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