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Thanks a lot Tom.<br>
The vop cover command works great.<br>
<br>
The dumpHeader is not a recognized keyword though.<br>
<br>
Cedric<br>
<br>
<br>
<div class="moz-cite-prefix">On 5/07/2016 19:23, Tom Goddard wrote:<br>
</div>
<blockquote
cite="mid:294B8C9F-C844-4CB2-90A9-FC6BBAF0DC47@sonic.net"
type="cite">
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Hi Cedric,
<div class=""><br class="">
</div>
<div class=""> Chimera does not automatically extend maps by
crystal symmetry like Coot (Chimera is primarily used for
electron microscopy maps). If your x-ray map is a unit cell you
can use Chimera command</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>vop
cover #1 atom #2</div>
<div class=""><br class="">
</div>
<div class="">where #1 is the model id of the map, and #2 is the
model id of the atomic model. If the map is just an asymmetric
unit and not a full unit cell then Chimera will have to use
space group symmetry to extend the map. It can only do that if
the space group symmetries are in the *.map CCP4 file. You can
see if those symmetries are present by using</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>vol
#0 dumpHeader true</div>
<div class=""><br class="">
</div>
<div class="">and looking for the symop header value in the
displayed output. Coot can probably produce the space group
symmetries from just the space group number (ispg header value),
but Chimera does not do that.</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Jul 4, 2016, at 6:11 AM, Cedric Govaerts
<<a moz-do-not-send="true"
href="mailto:cgovaert@ulb.ac.be" class="">cgovaert@ulb.ac.be</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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charset=windows-1252" class="">
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<p class="">Hi all,</p>
<p class="">I would like to use Chimera to show a 2FO-FC
or FO-FC electron density map (actually a tiny part of
it) obtained from COOT (or directly from the
refinement program).</p>
<p class="">If I open both the PDB file and the .map
file, they are correctly open except that the bounding
box from chimera truncate the map way to early.</p>
<p class="">That's because my PDB absolute coordinate
sit in the origin and it seem I cannot use negative
value for the boundaries of the volume/map.</p>
<p class="">How can I get the map to extend entirely
over my protein ?</p>
<p class=""><br class="">
</p>
<p class="">Thanks !</p>
<p class=""><br class="">
</p>
<p class="">Cedric<br class="">
</p>
<br class="">
<pre class="moz-signature" cols="72">--
Cedric Govaerts, Ph.D.
Universite Libre de Bruxelles
Campus Plaine. Phone :+32 2 650 53 77
Building BC, Room 1C4 203
Boulevard du Triomphe, Acces 2
1050 Brussels
Belgium<span id="cid:part1.3D665874.632F2BAF@ulb.ac.be"><lmhhpkhmepadlnpa.png></span>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://govaertslab.ulb.ac.be/">http://govaertslab.ulb.ac.be/</a></pre>
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</blockquote>
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<br class="">
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Cedric Govaerts, Ph.D.
Universite Libre de Bruxelles
Campus Plaine. Phone :+32 2 650 53 77
Building BC, Room 1C4 203
Boulevard du Triomphe, Acces 2
1050 Brussels
Belgium
<a class="moz-txt-link-freetext" href="http://govaertslab.ulb.ac.be/">http://govaertslab.ulb.ac.be/</a></pre>
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