<div dir="ltr"><div><div><div><div>Dear Pavel,<br><br></div>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.<br><br></div>Many thanks for your comments on this.<br></div>Best<br></div>Simone<br><br></div><div class="gmail_extra"><br><div class="gmail_quote">2016-12-03 4:54 GMT+01:00 Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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):<br>
<br>
Next Phenix nightly build (dev-2612 and up) will have a command line tool to compute map-model real-space difference maps.<br>
<br>
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:<br>
<br>
(F_obs, Phase_obs) - (F_calc, Phase_calc).<br>
<br>
The other map is computed using both spaces, and is analog of (F_obs-F_calc, Phase_obs); here no model phase is involved.<br>
<br>
I'm not sure which one of the two is better.<br>
<br>
Both maps are useful to locate ligands or yet not built pieces of the model (very much like in crystallography).<br>
<br>
Current limitations:<br>
- no GUI;<br>
- map must have origin at (0,0,0);<br>
- output file name can't be changed.<br>
<br>
To use:<br>
<br>
phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9<br>
<br>
which will output two maps: map_model_difference_1.ccp4 and map_model_difference_2.ccp4 .<br>
<br>
If proving ligand is the purpose to compute this map, then obviously it should not be present in model.pdb.<br>
<br>
In future (once fully tested) this will be integrated into phenix.real_space_refine.<br>
<br>
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!<br>
<br>
All the best,<br>
Pavel<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature">Dr. Simone Pellegrino<br>I.G.B.M.C.<br>1, Rue Laurent Fries<br>67404 Illkirch Cedex<br>France</div>
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