[3dem] Remove negative density from a map

Marin van Heel marin.vanheel at googlemail.com
Mon Apr 29 02:58:07 PDT 2013

Dear Max

If I understand you correctly, what you want is a simple threshold 
operation of the difference map. Threshold the negative values in the 
map to a minimum value of zero.  The imagic command "Threshold-image" 
will do the trick. (If you are not using imagic for this, first use 
em2em to convert your preferred MRC format to imagic and then to go back 
to your desired mrc format).


On 29-Apr-13 9:49 AM, 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
> Fax : +31 20 512 2029
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     Marin van Heel

     Professor of Cryo-EM Data Processing

     Leiden University
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