<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Gabriel,<div class=""><br class=""></div><div class=""> Coot automatically extends a map by crystal symmetry to cover the atomic model. Chimera does not do that. When you say the Coot exported map is misaligned and far from the PDB model, I’d guess the map position is correct only it has to be extended by crystal symmetry to cover the PDB model. This can be done with the Chimera “vop cover” command, for instance,</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>vop cover #1 atom #0</div><div class=""><br class=""></div><div class="">where #1 is the map and #0 is the PDB model. Here are the vop cover docs</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover" class="">https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover</a></div><div class=""><br class=""></div><div class="">You can then save the map using Volume Viewer menu File / Save Map As… so you have a copy that covers the PDB without needing to use crystal symmetry, or the command</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>volume #2 save mymap.mrc</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On May 22, 2018, at 10:38 AM, Gabriel Brandt <<a href="mailto:gbrandt@fandm.edu" class="">gbrandt@fandm.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><br class=""></div>Hi. I've always been able to work around this problem, but I do often have to work around it, so I was wondering whether there's an easier way.<div class=""><br class=""></div><div class="">Let's say I open a PDB file in Coot and export the map that it generates from the mtz file.</div><div class=""><br class=""></div><div class="">If I attempt to open this ccp4-formatted map in Chimera, the coordinates appear to transformed so that the model and map are wildly misaligned in space.</div><div class=""><br class=""></div><div class="">Normally, I work around this problem by using the map-generating feature in Phenix, which generates a model and map that align in Chimera. </div><div class=""><br class=""></div><div class="">However, in this case, I'm trying to compare the maps that Coot generates on the fly to the those produced by Phenix, so it would be nice to be able to export a map from Coot and open it in Chimera.</div><div class=""><br class=""></div><div class="">Thanks very much.</div><div class=""><br class=""></div><div class="">gsb</div><div class=""><br class=""></div><div class=""> <br class=""><div class="">
………………………………...<br class="">Gabriel Brandt<br class="">Assistant Professor<br class="">Department of Chemistry<br class="">Franklin & Marshall College<br class="">PO Box 3003<br class="">Lancaster, PA 17604<br class="">ph: 717.358.4846<br class=""><br class="">shipping address:<br class="">415 Harrisburg Ave<br class="">Lancaster, PA 17603<br class="">………………………………...
</div>
<br class=""></div></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>