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

Pavel Afonine pafonine at lbl.gov
Tue Mar 14 11:30:22 PDT 2017


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 
> <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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