OK. Knowing that and rereading the OP's question and your reply, I think that was the right answer. Apologies to CCP4 for accidentally cross-posting. eab On 05/12/2015 01:21 PM, Philip Kiser wrote:

There is a tool within PHENIX that prepares an mtz file for generation of an isomorphous difference map (scales the two datasets together, etc). I assumed that is what the OP was talking about.

On Tue, May 12, 2015 at 12:54 PM, Edward A. Berry mailto:[email protected]> wrote:

OK. I guess I was thinking of subtracting 2fo-Fc maps, which would give essentially (Fo1-Fo2) coefficients. But coming out of phenix it will be at least 2mFo-DFc, with different m's and D's for the two datasets. Makes it rather more complicated. eab

On 05/12/2015 11:58 AM, Philip Kiser wrote:

Good points. But also, the traditional isomorphous difference map is not as susceptible to model bias issues compared to a real space difference map (or a "vector" isomorphous difference map).

On Tue, May 12, 2015 at 11:37 AM, Edward A. Berry mailto:[email protected] mailto:[email protected]>> wrote:

On 05/12/2015 09:46 AM, Philip Kiser wrote:

crystallogrphy,

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.

Philip

Should be the same, due to linear property of the Fourier transform, EXCEPT for possible scaling differences and treatment of missing data. This latter could be significant, since presumably the traditional methods omits reflections unless present in both datasets, whereas in Tim's method each map will be made with all data available in that dataset. As a result, the largest coefficients in Tim's difference map might be the reflections which are absent in one map and present in the other. But if both have good completeness, it may not matter.

eab

On Tue, May 12, 2015 at 9:24 AM, Tim Gruene mailto:[email protected] mailto:[email protected]> mailto:[email protected] mailto:[email protected]>>> 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 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.

Regards, Tim

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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