[3dem] Remove negative density from a map

[Marcel Arheit]

Dear Max,

just to name another software solution. We implemented in 2dx
(2dx.org) a script for difference maps, that sets the negative
densities to zero before the subtraction. In 2dx you have the choice
of the classical method using CCP4 (as Martyn decribed) or a newer
method using Pyhton and its Matplotlib.

Regards,

Marcel

On Mon, Apr 29, 2013 at 12:26 PM, Daniel Castano Diez
<daniel.castano at unibas.ch> wrote:
> Hi Max,
>
> these kind of manipulations (pixelwise operations on volumes) are easy
> in Matlab  (or in the  Dynamo command line if you don't have a Matlab
> license), for instance in your case:
>
>  >> dread mymap.mrc a;  % reads your map into the Matlab/Dynamo workspace
>  >> a(a<0)=0;          % now it's just an array that you can manipulate
> from the command line and then write again into a .mrc file
>
> cheers,
> D.
>
>> 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/>
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>> Tel : +31 20 512 2022
>> Fax : +31 20 512 2029
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-- 
Marcel Arheit
Center for Cellular Imaging and Nanoanalytics (C-CINA)
Structural Biology and Biophysics, Biozentrum,
WRO-1058 Mattenstrasse 26
University Basel, CH-4058 Basel, Switzerland
Tel: +41 - 61 - 387 32 25 (office)
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