<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span style="font-size: 13px;" class="">Hi Simone,</span><div class=""><font size="2" class=""><br class=""></font></div><div class=""><font size="2" class="">the file (emd_8576) you get form EMDB is in ccp4 format (little nuances aside, essentially it’s all the same -- .ccp4, .map, .mrc), and then just use the command I quoted earlier.</font></div><div class=""><font size="2" class=""><br class=""></font></div><div class=""><font size="2" class="">Pavel<br class=""></font><div class=""><br style="font-size: 13px;" class=""><div style="font-size: 13px;"><blockquote type="cite" class=""><div class="">On Mar 16, 2017, at 05:56, Simone Pellegrino <<a href="mailto:simonpelle81@gmail.com" class="">simonpelle81@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Hi Pavel,<br class=""><br class=""></div>thanks for your mail. I first tried to run as a difference map in Coot (I was not doing so before, my mistake) but I still do not obtain th same as you. Could you please tell me how you get the ccp4 file? Do you go from the deposited .map file to .mtz and then from this to .ccp4 format using phenix?<br class=""></div><br class="">Many thanks for the help<br class=""><br class=""></div>Best<br class=""></div>Simone<br class=""><br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">2017-03-14 19:30 GMT+01:00 Pavel Afonine <span dir="ltr" class=""><<a href="mailto:pafonine@lbl.gov" target="_blank" class="">pafonine@lbl.gov</a>></span>:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000" class="">
Hi Simome,<br class="">
<br class="">
I get a very nice difference density for the ligand:<br class="">
<br class="">
<a class="m_1828675168750792930moz-txt-link-freetext" href="http://cci.lbl.gov/~afonine/tmp/coot.png" target="_blank">http://cci.lbl.gov/~afonine/<wbr class="">tmp/coot.png</a><br class="">
<br class="">
Command I used:<br class="">
<br class="">
phenix.real_space_diff_map 5umd_box.pdb 5umd_box.ccp4 resolution=3.2<br class="">
<br class="">
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 class="">
<br class="">
So.. all seems to work fine for me.<span class=""><br class="">
<br class="">
Pavel<br class="">
<br class="">
<div class="m_1828675168750792930moz-cite-prefix">On 3/14/17 08:42, Simone Pellegrino
wrote:<br class="">
</div>
</span><div class=""><div class="h5"><blockquote type="cite" class="">
<div dir="ltr" class="">
<div class="">
<div class="">
<div class="">
<div class="">Dear Pavel,<br class="">
<br class="">
</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 class="">
<br class="">
</div>
Many thanks for your comments on this.<br class="">
</div>
Best<br class="">
</div>
Simone<br class="">
<br class="">
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">2016-12-03 4:54 GMT+01:00 Pavel Afonine
<span dir="ltr" class=""><<a href="mailto:pafonine@lbl.gov" target="_blank" class="">pafonine@lbl.gov</a>></span>:<br class="">
<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 class="">
<br class="">
Next Phenix nightly build (dev-2612 and up) will have a
command line tool to compute map-model real-space difference
maps.<br class="">
<br class="">
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 class="">
<br class="">
(F_obs, Phase_obs) - (F_calc, Phase_calc).<br class="">
<br class="">
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 class="">
<br class="">
I'm not sure which one of the two is better.<br class="">
<br class="">
Both maps are useful to locate ligands or yet not built
pieces of the model (very much like in crystallography).<br class="">
<br class="">
Current limitations:<br class="">
- no GUI;<br class="">
- map must have origin at (0,0,0);<br class="">
- output file name can't be changed.<br class="">
<br class="">
To use:<br class="">
<br class="">
phenix.real_space_diff_map model.pdb map.ccp4 resolution=3.9<br class="">
<br class="">
which will output two maps: map_model_difference_1.ccp4 and
map_model_difference_2.ccp4 .<br class="">
<br class="">
If proving ligand is the purpose to compute this map, then
obviously it should not be present in model.pdb.<br class="">
<br class="">
In future (once fully tested) this will be integrated into
phenix.real_space_refine.<br class="">
<br class="">
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 class="">
<br class="">
All the best,<br class="">
Pavel<br class="">
<br class="">
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</blockquote>
</div>
<br class="">
<br clear="all" class="">
<br class="">
-- <br class="">
<div class="m_1828675168750792930gmail_signature" data-smartmail="gmail_signature">Dr.
Simone Pellegrino<br class="">
I.G.B.M.C.<br class="">
1, Rue Laurent Fries<br class="">
67404 Illkirch Cedex<br class="">
France</div>
</div>
</blockquote>
<br class="">
</div></div></div>
</blockquote></div><br class=""><br clear="all" class=""><br class="">-- <br class=""><div class="gmail_signature" data-smartmail="gmail_signature">Dr. Simone Pellegrino<br class="">I.G.B.M.C.<br class="">1, Rue Laurent Fries<br class="">67404 Illkirch Cedex<br class="">France</div>
</div>
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