[3dem] RE: Remove negative density from a map

[martyn.winn at stfc.ac.uk]

If it is a standard mrc map, then CCP4 has a number of map utilities that may be useful. I think this does what you want (?):

# Copy map and trim to single unit cell
mapmask mapin emd_5009_orig.map mapout emd_5009.map << eof
MODE mapin mapout
XYZLIM -47   47  -47   47  -47   47
eof

# Create a dummy mask
mapmask mapin emd_5009.map mskout emd_5009.msk << eof
MODE mapin mskout
MASK CUT -100.0
eof

# Reset negative values
mapmask mapin emd_5009.map mskin2 emd_5009.msk mapout emd_5009_out.map << eof
MODE mapin mskin2
SOLV ATTN 0.0
eof

It is a bit fiddly because it expects a mask covering a single unit cell, but it works for me on one example at least. Of course, I am sure there are other ways.

HTH
Martyn

*
*   Dr. Martyn Winn
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.
*   Tel: +44 1925 603455 (DL)   or   +44 1235 567865 (RcaH)
*   E-mail: martyn.winn at stfc.ac.uk       Skype: martyn.winn
*


> -----Original Message-----
> From: 3dem-bounces at ncmir.ucsd.edu [mailto:3dem-bounces at ncmir.ucsd.edu]
> On Behalf Of m.maletta at nki.nl
> Sent: 29 April 2013 09:49
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Remove negative density from a map
> 
> 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/>   |
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> m.maletta at nki.nl<mailto:m.maletta at nki.nl>
> Tel : +31 20 512 2022
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