<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi Catalin,</div><div><br></div><div> The Chimera molmap command creates a density map for a molecule using a grid that has its 3 axes aligned with the x, y, and z axes of the molecular data (atom coordinates) with padding 3 times the requested map resolution. This is described in the molmap documentation</div><div><br></div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html</a><div><br></div><div>The origin of the grid equals the x,y,z coordinates of the grid point at grid index 0,0,0. That origin position (floating point values) is saved in an MRC 2000 file in the xorigin, yorigin, zorigin header fields. </div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>http://www2.mrc-lmb.cam.ac.uk/image2000.html</div><div><br></div><div>It cannot be saved in the nxstart,nystart,nzstart header fields since those are integer values and can't accomodate the exact floating point origin. Here's the Chimera Python source code that reads MRC files if you want more details of how that is handled.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/VolumeData/mrc/mrc_format.py</div><div><br></div><div> Tom</div><div><br><div><br></div><div><br><div><div>On Jul 8, 2013, at 1:08 PM, Catalin Buiu wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="background-color: rgb(255, 255, 255); font-family: 'times new roman', 'new york', times, serif; font-size: 12pt; "><div><font face="times new roman, new york, times, serif">Hello all,</font></div><div><font face="times new roman, new york, times, serif"><br></font></div><div><font face="times new roman, new york, times, serif">I have the following problem: when I use molmap to generate </font></div><div><font face="times new roman, new york, times, serif">a map from an atomic structure, the result is fine: both align.</font></div><div><font face="times new roman, new york, times, serif">When I use another (Matlab) program to generate the map, the two,</font></div><div><font face="times new roman, new york, times, serif">when opened in Chimera do not align anymore.</font></div><div><font face="times new roman, new york, times, serif">My question is how molmap generates an origin index such that</font></div><div><font face="times new
roman, new york, times, serif">both the map and the structure do align and how Chimera reads (and converts)</font></div><div><font face="times new roman, new york, times, serif">the xyz origin data from the MRC file?</font></div><div><font face="times new roman, new york, times, serif"><br></font></div><div><font face="times new roman, new york, times, serif">Thank you.</font></div><div><font face="times new roman, new york, times, serif"><br></font></div><div><font face="times new roman, new york, times, serif">Catalin Buiu</font></div><div><font face="times new roman, new york, times, serif">University of Bucharest, Romania</font></div></div></div>_______________________________________________<br>Chimera-users mailing list<br>Chimera-users@cgl.ucsf.edu<br>http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div></div></body></html>