<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Tom<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Thanks for the clarification. It turns out I had no idea how the new origin fields are interpreted. It is also not clear from the limited documentation how it should be interpreted and there are no example images to see how it is done. So I decided to just follow your explanation and fix it in Bsoft such that it displays correctly in Chimera.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Thanks again</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Bernard</DIV><DIV><BR><DIV><DIV>On Oct 23, 2007, at 2:24 PM, Tom Goddard wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Bernard,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>The Chimera origin reported in the Volume Viewer dialog is not the array index of physical origin.<SPAN class="Apple-converted-space"> </SPAN>It is the physical coordinate of array index 0,0,0.<SPAN class="Apple-converted-space"> </SPAN>So it is the inverse of how you are interpreting it.<SPAN class="Apple-converted-space"> </SPAN>We've been using this definition since about 2000, before your 2006 paper on conventions for EM maps.<SPAN class="Apple-converted-space"> </SPAN>With this understanding your example of a 100^3 map with physical origin at array index (50,50,50) and 2 angstroms/voxel the index (0,0,0) physical coordinate is (-100,-100,-100) which you say Chimera reports for a CCP4 map.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Chimera uses the xorigin, yorigin, zorigin header values (words 50-52) in MRC2000 format instead of the nxstart, nystart, nzstart header values (words 5-7).<SPAN class="Apple-converted-space"> </SPAN>You probably have (50,50,50) in the xyz origin fields while</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera expects (-100,-100,-100) in those fields.<SPAN class="Apple-converted-space"> </SPAN>The MRC documentation</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN><A href="http://www2.mrc-lmb.cam.ac.uk/image2000.html">http://www2.mrc-lmb.cam.ac.uk/image2000.html</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">unfortunately does not describe the meaning of those origin fields, though I suspect your interpretation is correct as it agrees with nxstart,nystart,nzstart definition and would just provide floating point equivalents of those integer values.<SPAN class="Apple-converted-space"> </SPAN>Perhaps there is better MRC documentation defining xorigin,yorigin, zorigin.<SPAN class="Apple-converted-space"> </SPAN>Chimera writes MRC2000 files and fills the origin fields with the physical coordinate of index (0,0,0).</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>These different interpretations of the meaning of the origin fields are a big problem.<SPAN class="Apple-converted-space"> </SPAN>How are the xorigin,yorigin,zorigin fields in MRC2000 actually being used?<SPAN class="Apple-converted-space"> </SPAN>I know Chimera and EMAN both interpret it as a physical coordinate of array index (0,0,0).<SPAN class="Apple-converted-space"> </SPAN>From your comments I assume BSOFT interpets it as the array index of the physical coordinate origin.<SPAN class="Apple-converted-space"> </SPAN>What other software is using these fields and how do they interpret it?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>It would be a big problem to change the origin definition in Chimera because users have written many MRC2000 files using Chimera that would no longer be positioned correctly if the meaning of the origin fields is changed.<SPAN class="Apple-converted-space"> </SPAN>Chimera does not write information in the MRC labels header fields indicating which version of Chimera wrote the file.<SPAN class="Apple-converted-space"> </SPAN>That was a mistake.<SPAN class="Apple-converted-space"> </SPAN>So there is no way of telling which interpretation should be used for a Chimera-written MRC file.<SPAN class="Apple-converted-space"> </SPAN>EMAN currently writes a label line saying EMAN and the date and time the file was written.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Tom</DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Bernard Heymann, Research Fellow</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Rm 1515, 50 South Dr., MSC 8025, NIAMS, NIH</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Bethesda MD 20892-8025</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Tel. 301-451-8241, Fax. 301-480-7629</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></BODY></HTML>