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<p>Hi Stephan</p>
<p>I am not an expert at all but I think I was having similar
problems as you are mentioning...</p>
<p>In our case uploading the file to the pdb validation/deposition
systems and getting back either of the generated files was nicely
fixing our problems... Maybe you have already tried this simple
thing or maybe is worthy to give it a trial<br>
</p>
<ul>
<li> (validation is quicker: upload summary "converted file name")
<br>
</li>
<li>(deposition requires to fill in stuff with whole sequence:
re-upload files "converted file name")</li>
</ul>
<p>(Although the pdb_ extract tool was not useful for us right now
as somehow some weird stuff in the loops was appearing...)<br>
</p>
<p>Regards</p>
<p>Marta <br>
</p>
<p>P.D. Also working here with huge molecules <br>
</p>
<div class="moz-cite-prefix">On 04/03/2020 09:58, Tetter Stephan
wrote: <br>
</div>
<blockquote type="cite"
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<div style="color: rgb(0, 0, 0);">Dear all,<br>
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<p><br>
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<p>I am having an issue with secondary structure display.
I am real-space refining a set of 120 chains in phenix.
Of these, only 10 are unique, the rest is
symmetry-related. Thus, I define secondary structure
elements for the 10 unique chains only. The output pdb
file header contains the secondary structure elements as
imposed during refinement. Displaying this pdb file in
ChimeraX shows the right secondary structure. The mmcif
file instead, whether I use the phenix output or
generate it from the pdb myself, displays different,
non-sensical structures. Secondary structure is shown in
loop regions, and some actual strands and helices not
recognized at all. This artifact is only shown for the
10 subunits with secondary structure definitions, the
other subunits show no secondary structure at all, thus
something is read in, but not correctly, apparently. Any
idea what the problem could be? Could the size of the
complex be an issue?</p>
<p><br>
</p>
<p>The attachments show the lines from the two file types
concerning secondary structure definitions.
<br>
</p>
<p><br>
</p>
<p>Kind regards, <br>
</p>
<p><br>
</p>
<p>Stephan <br>
</p>
<p><br>
</p>
<p><br>
</p>
<p><br>
</p>
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<br>
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