[Chimera-users] fit molecule with Laplacian filtered map

Tom Goddard goddard at sonic.net
Wed Aug 31 20:17:56 PDT 2011

Hi Noboru,

   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.


> Hello,
> 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.
> Noboru

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