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

Simone Pellegrino simonpelle81 at gmail.com
Thu Mar 16 05:56:12 PDT 2017

Hi Pavel,

thanks for your mail. I first tried to run as a difference map in Coot (I
was not doing so before, my mistake) but I still do not obtain th same as
you. Could you please tell me how you get the ccp4 file? Do you go from the
deposited .map file to .mtz and then from this to .ccp4 format using phenix?

Many thanks for the help


2017-03-14 19:30 GMT+01:00 Pavel Afonine <pafonine at lbl.gov>:

> Hi Simome,
> I get a very nice difference density for the ligand:
> http://cci.lbl.gov/~afonine/tmp/coot.png
> Command I used:
> phenix.real_space_diff_map 5umd_box.pdb 5umd_box.ccp4 resolution=3.2
> Make sure to use map_model_difference_1.ccp4 as it seems to be better than
> the seconds map and also load it into Coot as a difference map.
> So.. all seems to work fine for me.
> Pavel
> On 3/14/17 08:42, Simone Pellegrino wrote:
> 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.
> Best
> Simone
> 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
> I.G.B.M.C.
> 1, Rue Laurent Fries
> 67404 Illkirch Cedex
> France

Dr. Simone Pellegrino
1, Rue Laurent Fries
67404 Illkirch Cedex
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