[3dem] Remove negative density from a map

[Marin van Heel]

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).
Cheers
Marin

=====================================================

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
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem


-- 
================================================================

     Marin van Heel


     Professor of Cryo-EM Data Processing

     Leiden University
     Cell Observatory
     NeCEN Building Room 05.27
     Einsteinweg 55
     2333 CC Leiden
     The Netherlands
      
     Tel. NL:     + 31 (0) 715271424
     Mobile NL:   + 31 (0) 652736618
     Skype:       Marin.van.Heel

     and:

     Professor of Structural Biology

     Imperial College London
     Faculty of Natural Sciences
     Division of Molecular Biosciences
     Biochemistry Building (Room 512)
     South Kensington Campus
     London SW7 2AZ,  UK
  
     Tel. UK:   + 44 (0) 20 75945316
     Mobile:    + 44 (0) 7941540625

     email:  marin.vanheel(A_T)gmail.com
     email:  m.vanheel(A_T)ic.ac.uk
     and:    mvh.office(A_T)gmail.com


I receive many emails per day and, although I try, there is no guarantee that I will actually read each incoming email. Moreover, our Spam filters can be strikt and sometimes make legitimate emails disappear (try the gmail accounts, alternatively)