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

Simone Pellegrino simonpelle81 at gmail.com
Tue Mar 14 08:42:59 PDT 2017

Dear Pavel,

I am trying to obtain a difference map for the recent pdb ID: 5umd. I took
the map deposited as emd_8576 and tried to obtain the difference map as you
suggest. Unfortunately I have several blobs appearing but nothing where the
ligand (an antibiotic binding the ribosome) was (I removed it from the
initial pdb prior running the script). Also I find that it is difficult to
interpret the two maps coming as output.

Many thanks for your comments on this.

2016-12-03 4:54 GMT+01:00 Pavel Afonine <pafonine at lbl.gov>:

> 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
> phenix.real_space_refine.
> 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,
> Pavel
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Dr. Simone Pellegrino
1, Rue Laurent Fries
67404 Illkirch Cedex
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