[3dem] Remove negative density from a map

[Steven Ludtke]

Just to round off the many replies, in EMAN2:

e2proc3d.py input.mrc output.mrc --process=threshold.clampminmax:minval=0:maxval=<something big>

(replace <something big> with a number largest than the biggest value in your map)

On Apr 29, 2013, at 3:49 AM, "m.maletta at nki.nl" <m.maletta at nki.nl> wrote:

> Dear all
> Does anybody know how to remove negative density (set to zero) from a mrc map?
> I subtracted two structures to highlight a factor and the negative peaks are making my life miserable.
> Best
> Max
> 
> __________________________________
> Massimiliano Maletta
> post-doc in
> NKI Netherlands Cancer Institute -Antoni van Leeuwenhoek Hospital Plesmanlaan 121 B6 1066CX Amsterdam
> group of Peter Peters
> www.nki.nl/research/peters/<http://www.nki.nl/research/peters/>   | www.necen.nl<http://www.necen.nl/>
> m.maletta at nki.nl<mailto:m.maletta at nki.nl>
> Tel : +31 20 512 2022
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----------------------------------------------------------------------------
Steven Ludtke, Ph.D.
Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)
Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)
Co-Director CIBR Center                          (www.bcm.edu/research/cibr)
Baylor College of Medicine                             
sludtke at bcm.edu