<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=""> The reason your map surface shows the triangulation is because the grid spacing is large. You made the map with molmap with 30A resolution. By default molmap sets the grid spacing to 1/3 of the requested resolution, so 10 Angstroms in this case. Apparently this is too coarse for your needs. So spedify a finer grid spacing in the molmap command. For instance</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>molmap #0 30 gridSpacing 3</div><div class=""><br class=""></div><div class="">to produce 30 A resolution with 3 A grid spacing. Here is the molmap documentation</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/current/docs/UsersGuide/midas/molmap.html" class="">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/molmap.html</a></div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 16, 2015, at 8:45 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="">Hi Tom,<div class="">It seems that the low-resolution (about 30A) map generated from atomic model by “molmap" has many artifacts on its surface (see first attached figure), and I can see many rectangle signatures of it in Fourier space (see 2nd attached figure) so that I can not use it as the start map for further reconstruction.</div><div class="">Please tell me how can I get rid of this. Thank you!</div><div class=""><br class=""></div><div class="">Best wishes!</div><div class=""><br class=""></div><div class=""><br class=""></div><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="">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=""><span id="cid:6D899A50-8FA8-47B2-9744-8FCE753448D2"><molmap_30A.png></span><span id="cid:525197D5-E7F7-44E5-924A-E769F12727D7"><FFT.png></span></div></div>
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<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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<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Apr 15, 2015, at 1:28 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="">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 class=""><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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