<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=""><div class="">You can crop a map using volume dialog menu Features / Region Bounds, then save it with volume dialog File / Save Map As…. Other Chimera map capabilities are described in the Guide to Volume Data Display in Chimera:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html" class="">http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><br class=""><div><blockquote type="cite" class=""><div class="">On Jun 23, 2015, at 7:52 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="">Adding to the previous one.<div class="">the map I want to convert has a same pixel size with the data set. So maybe the question could be that how can I cutting the boundaries of the map to fit the size of reconstruction images. </div><div class=""><br class=""></div><div class="">Thanks!</div><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=""><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<br class=""><br class=""></div></div>
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<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Jun 24, 2015, at 10:44 AM, 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="">Hi, Tom<div class="">An another question, </div><div class="">I want to make a reference map for reconstruction, here I have a map but with different map size from my raw image, how can I scale the map dimensions into a specific value without changing the centre coordinates.</div><div class="">Thanks!</div><div class=""><br class=""><div 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=""><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<br class=""><br class=""></div></div>
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<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Jun 24, 2015, at 2:00 AM, Tom Goddard 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="">If you used the Chimera Segment Map dialog (volume dialog menu Tools / Segment Map) then you select a segment (ctrl click on it) and use Segment Map menu entry Regions / Mean and SD. If you segmented the map by some other means and have the pieces as separate maps use volume dialog menu Tools / Measure Mean, SD, RMS.<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 class=""><blockquote type="cite" class=""><div class="">On Jun 23, 2015, at 6:42 AM, 李智海 wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class="">Here I want to evaluate the flexibility of variable domains of a density map. How can I quantify the mean intensity of segmented parts by Chimera? Thanks!</div><div class=""><br class=""></div><div class="">Best wishes!</div><div class=""><br class=""><div class=""><div 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=""><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<br class=""><br class="">Ph.D student in State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics.<br class="">School of Life Sciences, Xiamen University.<br class="">Xiang'an Road(South), Xiang'an District, Xiamen City,<br class="">Fujian Province, China.</div></div>
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