<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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 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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<div bgcolor="#FFFFFF" text="#000000" class=""><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 class="moz-txt-link-freetext" href="http://govaertslab.ulb.ac.be/">http://govaertslab.ulb.ac.be/</a></pre></div>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>