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Hi Tristan,<br>
<br>
in recent Phenix versions we replaced "kick map" option with a
generalized (and more sophisticated) concept that we call FEM -
Feature Enhanced Map. The paper is scheduled to appear in Acta D:<br>
<a class="moz-txt-link-freetext" href="http://journals.iucr.org/d/services/readerservices.html">http://journals.iucr.org/d/services/readerservices.html</a><br>
<br>
Meanwhile you can read through the set of pages that explain the
concept and show examples:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/fem_06MAY2014.pdf">http://www.phenix-online.org/presentations/fem_06MAY2014.pdf</a><br>
<br>
Let me know if you have questions!<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 2/5/15 1:12 AM, Tristan Croll wrote:<br>
</div>
<blockquote cite="mid:1423127557881.55828@qut.edu.au" type="cite">
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<p>My previous email was hung up in moderation due to my
attaching a jpeg that tripped the size limit. In any case,
I've done a bit more testing and the problem doesn't actually
originate in the fill_missing_f_obs, but in the kicked map
algorithm. If, as per the attached parameter file, I have a
kicked map in the to-do list, every map past that point is
garbled (the kicked map itself appears fine). Set kicked to
False, and all maps come out looking normal.</p>
<p><br>
</p>
<p>I should also note that the sharpening_b_factor parameter
seems inverted from the normal convention: a negative value
gives smoothing rather than sharpening.</p>
<p><br>
</p>
<p>Cheers,</p>
<p><br>
</p>
<p>Tristan<br>
</p>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
color="#000000" face="Calibri, sans-serif"><b>From:</b>
Tristan Croll<br>
<b>Sent:</b> Thursday, 5 February 2015 3:47 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>
<b>Subject:</b> Strange behaviour of phenix.maps
fill_missing_f_obs</font>
<div>�</div>
</div>
<div>
<div id="divtagdefaultwrapper" style="font-size:12pt;
color:#000000; background-color:#FFFFFF;
font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi,</p>
<p><br>
</p>
<p>I'm working on a package that makes scripted calls to
phenix.refine to generate a series of ccp4 formatted
maps, and have run into an odd problem. Using the
attached parameter file I get a series of perfectly
normal-looking maps, except in the case of the filled
2mFo-DFc map (test-3_2mFo-DFc_fill.ccp4 - the
second-last map generated). This comes out as a series
of disconnected blobs (it looks rather like a mFo-DFc
map, but it doesn't match the actual mFo-DFc
map).�When�I�take�the�resulting .mtz file and generate
the filled map in�Coot (with or without omission of
Rfree flags), on the other hand,�it seems to come out
fine.� There are no�error messages in the log,�but I
suspect�the� default method to fill in the missing F_obs
may be returning
<em>only</em>�the missing F_obs?</p>
<p><br>
</p>
<p>I've attached a small example image. Red wireframe is
the 2mFo-DFc unfilled map at 1 sigma; green translucent
is the 2mFo-DFc filled map at 1 sigma; yellow is the
mFo-DFc map at 2 sigma.</p>
<p><br>
</p>
<p>The test structure I'm using is nothing special: 3WSY,
picked more-or-less at random off the protein data bank.
Phenix version is 1.9.1692, installed in Fedora 21.</p>
<p><br>
</p>
<p>Have I done something wrong that I'm just not seeing,
or is there a bug here?<br>
</p>
<p><br>
</p>
<p>Thanks,</p>
<p><br>
</p>
<p>Tristan<br>
</p>
</div>
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<br>
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