[phenixbb] how to generate an isomorphous difference map

Pavel Afonine pafonine at lbl.gov
Wed May 13 09:27:24 PDT 2015


I infer you are trying to compute (Fobs1-Fobs1, model_phase) Fourier map.

You can do it using command line phenix.fobs_minus_fobs_map or GUI (Maps 
-> Isomorphous difference map).

For using in Coot, no need to transform into ccp4 map: Coot can contour 
any map at positive and negative levels.

For using in Pymol: convert your map into ccp4 format using 
phenix.mtz2map (command line) or GUI (Maps -> FFT map coefficients).

Hope this helps.

On 5/12/15 5:43 AM, 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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