Hi Greg, A Laplacian filter is simple to implement. I'll see if I can add it to the "vop" command later this week. The Laplacian filter roughly speaking does edge detection so alignments of filtered maps will try to match the boundaries of the objects. The Laplacian is a sum of second derivatives and will be useless on noisy data (e.g. any tomography) unless you smooth the data first with for instance a Gaussian filter. Tom Grigore Pintilie wrote:

Hi,

Just wondering if it might be possible to apply a Laplacian filter on a density map in chimera. The reason I'm asking is that if the cross-correlation is computed with laplacian-filtered maps it gives more robust results for the correct alignments vs. non-correct alignments.

Thanks,

Greg _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Tom, Thank you very much for this implementation, I will experiment with it. You're absolutely right that the Laplacian is very sensitive to noise, point well made! Greg On Fri, Nov 21, 2008 at 6:28 PM, Tom Goddard <goddard@cgl.ucsf.edu> wrote:

Hi Greg,

I've added volume Laplacian calculation to Chimera. It is available via the volume operation "vop" command. To calculate the Laplacian of model #3 use

vop #3 laplacian

It will create a new volume data set. This will be in tonight's Chimera 1.4 daily builds.

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

Tom

Tom Goddard wrote:

...

Hi Greg,

A Laplacian filter is simple to implement. I'll see if I can add it to the "vop" command later this week. The Laplacian filter roughly speaking does edge detection so alignments of filtered maps will try to match the boundaries of the objects. The Laplacian is a sum of second derivatives and will be useless on noisy data (e.g. any tomography) unless you smooth the data first with for instance a Gaussian filter.

Tom

Grigore Pintilie wrote:

...

Hi,

Just wondering if it might be possible to apply a Laplacian filter on a density map in chimera. The reason I'm asking is that if the cross-correlation is computed with laplacian-filtered maps it gives more robust results for the correct alignments vs. non-correct alignments.

Thanks,

Greg