<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 Huiya,<div class=""><br class=""></div><div class=""> There is a list of Chimera Python scripts, many that read volume data here</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts" class="">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a></div><div class=""><br class=""></div><div class="">and this readvol.py one shows how to get the 3d matrix as a numpy array, basic m = v.matrix() or m = v.full_matrix(), full_matrix() gives the full 3d data even if it is being shown subsampled, e.g. at step 2,</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/readvol.py" class="">http://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/readvol.py</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Aug 21, 2019, at 9:38 AM, Huiya Zhou <<a href="mailto:huiya@tamu.edu" class="">huiya@tamu.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; -webkit-line-break: after-white-space;" class="">Hello,<div class=""><br class=""></div><div class="">I am trying to use UCSF Chimera to analysis cry-EM density maps. I would like to read a density map (for example: a .mrc file) in python script and get the array (or a three dimensional matrix) of all voxels of this density map. How could I realize this?</div><div class=""><br class=""></div><div class="">By the way, I tried to learn some basic chimera functions which can be used in python on this website:</div><div class=""><a href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html" class="">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html</a></div><div class="">However, it seems this website can’t be opened and it shows me a blank page.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Best,</div><div class="">Huiya</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>