[phenixbb] difference map for cryo-EM (cryo-EM map minus model map)

Pavel Afonine pafonine at lbl.gov
Fri Dec 2 19:54:51 PST 2016

For those practicing cryo-EM and tending to use Phenix nightly builds, 
as well as in response to a recent post (Re: [phenixbb] difference map 
based on the cryo-EM map):

Next Phenix nightly build (dev-2612 and up) will have a command line 
tool to compute map-model real-space difference maps.

One map is computed in real space: cryo-EM map minus model calculated 
map; it is locally scaled in some complex way to account for local 
variations and possibly poorly refined B-factors. In terms of reciprocal 
space it is an analog of:

(F_obs, Phase_obs) - (F_calc, Phase_calc).

The other map is computed using both spaces, and is analog of 
(F_obs-F_calc, Phase_obs); here no model phase is involved.

I'm not sure which one of the two is better.

Both maps are useful to locate ligands or yet not built pieces of the 
model (very much like in crystallography).

Current limitations:
- no GUI;
- map must have origin at (0,0,0);
- output file name can't be changed.

To use:

phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9

which will output two maps: map_model_difference_1.ccp4 and 
map_model_difference_2.ccp4 .

If proving ligand is the purpose to compute this map, then obviously it 
should not be present in model.pdb.

In future (once fully tested) this will be integrated into 

The tool is 10 hours old and tested on just one model (5l4g, 
emd_4002.map), so bugs are not unexpected. Any feedback is welcome!

All the best,

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