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Hi Tofayel,<br>
<br>
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style="font-size:10pt;color:#000000;font-family:Verdana,Geneva,sans-serif;"
dir="ltr">I am trying to refine a complete virus pdb structure
(possessing icosahedral symmetry) in a cryo-EM map using
phenix.real_space_refine. The run fails complaining "Multi-model
PDB (with MODEL-ENDMDL) is not supported". So, I followed a
previous post in phenixbb: <a
href="http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html"
id="LPlnk272827" previewremoved="true" moz-do-not-send="true">
http://www.phenix-online.org/pipermail/phenixbb/2011-May/017079.html</a>
and merged multiple models into one </div>
</blockquote>
<br>
perhaps the advice you quote above is getting outdated a bit (though
still valid!). Yes, most Phenix tools can't do much with multi-model
files. In your case you can convert your multi-model file into a one
model file where all the models become new chains.<br>
<br>
phenix.models_as_chains<br>
<br>
should do it for you.<br>
<br>
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<p style="margin-bottom: 0in">but faced following problems:
</p>
<p style="margin-bottom: 0in"><br>
</p>
<p style="margin-bottom: 0in">1. This merged file is unreadable
in UCSF Chimera.</p>
</div>
</blockquote>
<br>
I guess you better talk to Chimera developers unless it is clearly
fault of Phenix.<br>
<br>
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<p style="margin-bottom: 0in">2. The secondary structure
definition in the PDB file�header is not recognizable anymore
in Phenix.</p>
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</blockquote>
<br>
Please send us an example and we will investigate!<br>
<br>
<blockquote type="cite"
cite="mid:SIXPR0199MB064941F1F54659544783436BE3D20@SIXPR0199MB0649.apcprd01.prod.exchangelabs.com">
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<p style="margin-bottom: 0in">In my understanding, both the
problems are arising�due to�PDB format's inability to handle
more than 62 chains and 99999 atoms in a file. </p>
</div>
</blockquote>
<br>
With two-letter chain id and hybrid36 (both are used in Phenix) this
is not the case, you can have way more chains and atoms. And if you
go to mmCIF (which is the standard, and also supported in Phenix),
then these limitations are nonexistent.<br>
<br>
Let us know if you have any questions or need help!<br>
<br>
Pavel<br>
<br>
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