[phenixbb] difference map for cryo-EM (cryo-EM map minus model map)
pafonine at lbl.gov
Tue Mar 14 11:30:22 PDT 2017
I get a very nice difference density for the ligand:
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.
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.
> 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
> 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,
> phenixbb mailing list
> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
> Unsubscribe: phenixbb-leave at phenix-online.org
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> Dr. Simone Pellegrino
> 1, Rue Laurent Fries
> 67404 Illkirch Cedex
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