[phenixbb] how to generate an isomorphous difference map

Tim Gruene tg at shelx.uni-ac.gwdg.de
Tue May 12 06:24:10 PDT 2015

Dear crystallogrphy,

you can open the PDB file with Coot, then use File -> Open MTZ to read one
mtz-file after the other into Coot. Coot will offer to generate the map
coefficients from the previously loaded PDB file.

Once you have both maps, you can go to Extensions -> Maps -> Make a Difference
Map to create the difference map.

In order to see both positive and negative density, you choose Extensions ->
Maps -> Set Map is a Difference Map.


On Tue, May 12, 2015 at 08:43:45PM +0800, crystallogrphy wrote:
> Hi,
> I am trying to generate an isomorphous difference map with phenix GUI. I
> input reflection 1 and 2 with mtz format and a PDB model, I got an MTZ
> format map file. Because I want to load it to coot or pymol with negative
> and positive density, I need to transform this mtz map to ccp4 map.
> However, FFT map cannot work.
> Does any know how can I get a ccp4 format maps with positive or negative
> density?
> Thanks!

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Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149


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