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
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]
-- Dr. Simone Pellegrino I.G.B.M.C. 1, Rue Laurent Fries 67404 Illkirch Cedex France