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

Pavel Afonine pafonine at lbl.gov
Tue Mar 14 10:55:41 PDT 2017

Hi Simone,

what's the ligand id (chain name, residue name and number)? Once I have 
it I will get pdb and map files off the data based and run the program 
and see what's happening.


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 
> <mailto: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

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