<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 Zhihai,<div class=""><br class=""></div><div class=""> If you want the map computed from an atomic model but on a grid that matches a reference map then you should compute the map with molmap and then resample it on the reference map grid. If #0 is the atomic model and #1 the reference map.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>molmap #0 8 edgePadding 50</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>vop resample #0 onGrid #1</div><div class=""><br class=""></div><div class="">Here the 8 is the resolution for the computed map and 50 Angstroms controls how far beyond the molecule bounding to compute the map.</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><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 13, 2015, at 9:00 PM, 李智海 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=""><div class="">hi,</div><div class="">here I want to generate a density map from a atomic model in Chimera, then convert the generating map into .pif file to do as the initial map performing in Auto3dem.</div><div class="">I have met some questions to successfully finish these work.</div><div class=""><br class=""></div><div class="">1.How can I generate a mol-map from a fitting model with identical dimensions, center coordinates and pixel size of its reference map. I have tried to use “Fit in map”, but the generating map differed from its fitted map in the map size.</div><div class=""><br class=""></div><div class="">2. The mrc map created in Chimera has dimension of even number of columns. If I set the column number to odd number, is it ok (for example, if the origin is off by half pixel?). The reason I am asking such a question is that I will convert this mol-map to pif format, and pif format map has dimension of odd number columns. </div><div class=""><br class=""></div><div class=""> </div><div class="">Thanks in advanced!</div><div class=""><br class=""></div>Best wishes!<div class=""><br class=""><div apple-content-edited="true" class="">
<div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Zhihai Li</div><div style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><br class=""><br class=""></div></div>
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