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Hi Simome,<br>
<br>
I get a very nice difference density for the ligand:<br>
<br>
<a class="moz-txt-link-freetext" href="http://cci.lbl.gov/~afonine/tmp/coot.png">http://cci.lbl.gov/~afonine/tmp/coot.png</a><br>
<br>
Command I used:<br>
<br>
phenix.real_space_diff_map 5umd_box.pdb 5umd_box.ccp4 resolution=3.2<br>
<br>
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.<br>
<br>
So.. all seems to work fine for me.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 3/14/17 08:42, Simone Pellegrino
wrote:<br>
</div>
<blockquote
cite="mid:CA+8MOGmmDWEOoF_1OqpEVTwtyewPDruoVihBfyV_CoT=CmYBug@mail.gmail.com"
type="cite">
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<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 moz-do-not-send="true"
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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</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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