<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Yaowang,<div class=""><br class=""></div><div class=""> The Chimera Volume Viewer voxel size setting (menu Features / Coordinates) changes the spacing between grid points. It does not change the map intensity values. If it appears to be wrong by a factor of 2 when compared to a PDB file then the voxel size is definitely. I would not just guess that it is a factor of 2 too small — you should find out from whoever did the reconstruction what the correct value is. But if 2.11A is the correct size than your fitting is fine.</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 class=""><br class=""></div><div class=""><div><blockquote type="cite" class=""><div class="">On Nov 23, 2015, at 1:31 AM, Yaowang Li wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><span style="font-size:12.8px" class="">Dear all,</span><br style="font-size:12.8px" class=""><br style="font-size:12.8px" class=""><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">I faced a scale problem when I was trying to fit the density map.</span><br style="font-size:12.8px" class=""><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">A density map was reconstructed from a set of projections which their</span><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">magnitude are 1.055A/pixel, with a reference model that is 1.055 A/voxel</span><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">and 5 A in resolution. However the pdb file cannot fit into the map</span><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">because the map is too much small. So I have to change the voxel size to</span><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">double and then can be fitted.</span><br style="font-size:12.8px" class=""><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">Here I changed the voxel size, I think it changed the scale for the</span><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">density. So i just worried about the fitting result.</span><br style="font-size:12.8px" class=""><br style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">thanks</span><br class=""></div></div></blockquote></div><br class=""></div></div></body></html>