[phenixbb] how to generate an isomorphous difference map
pdk7 at case.edu
Tue May 12 06:46:43 PDT 2015
If you did everything correctly, you should be able to directly calculate
the difference map in Coot from the MTZ file generated by PHENIX. You would
need to open it with "Open MTZ" rather than "Auto open MTZ" and then select
the appropriate map coefficients. Note that what Tim described (a real
space difference map) is technically different from the traditional
isomorphous difference map where the SF amplitudes of the two data sets are
subtracted prior to the map calculation.
On Tue, May 12, 2015 at 9:24 AM, Tim Gruene <tg at shelx.uni-ac.gwdg.de> wrote:
> 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
> 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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