<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Yeping,<div class=""><br class=""></div><div class="">  That figure from Nature uses ChimeraX, not Chimera.  ChimeraX is the successor to Chimera.  ChimeraX has better lighting.  In ChimeraX uses soft lighting,  Also make sure step size is 1 in the Volume Viewer panel to show data at full resolution.  And use a high enough threshold level so helices have space between them.</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><br class=""><blockquote type="cite" class=""><div class="">On Aug 4, 2020, at 9:45 AM, sunyeping <<a href="mailto:sunyeping@aliyun.com" class="">sunyeping@aliyun.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="__aliyun_email_body_block"><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class="">Dear all,</span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class=""><br class=""></span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px;" class="">I am trying to learn preparing publishable figures of cryo-EM protein structure. I try to reproduce a figure (fig. 4A) from a paper published in Nature (<a href="https://doi.org/10.1038/s41586-020-2571-7" class="">https://doi.org/10.1038/s41586-020-2571-7</a>).</span></div><div style="clear:both;" class="">Could you please find the original figure in the publication and the one I prepared in the following linkļ¼Ÿ</div><div style="clear:both;" class=""><br class=""></div><div style="clear:both;" class=""><a href="https://drive.google.com/file/d/1dwQYT9-bGbs7OHi8e351SmE0FYr6FLK4/view?usp=sharing" class="">https://drive.google.com/file/d/1dwQYT9-bGbs7OHi8e351SmE0FYr6FLK4/view?usp=sharing</a></div><div style="clear:both;" class=""><br class=""></div><div style="clear:both;" class="">The original figure (a) is for EMD-22156. I download the map for <span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; text-align: start; text-indent: 0px; text-transform: none; widows: 2; background-color: rgb(255, 255, 255); float: none; display: inline;" class="">EMD-22156 form <a href="https://www.ebi.ac.uk/pdbe/emdb/" class="">https://www.ebi.ac.uk/pdbe/emdb/</a>, loaded it in Chimera, adjusted the range, hide the dusted, performed segmentation, and get images like (b). </span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; text-align: start; text-indent: 0px; text-transform: none; widows: 2; background-color: rgb(255, 255, 255); float: none; display: inline;" class="">The orignal figure (a) has plenty of structural detailed, and the helix can be clearly seen, but the images I prepared do not like that and look ugly. </span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; text-align: start; text-indent: 0px; text-transform: none; widows: 2; background-color: rgb(255, 255, 255); float: none; display: inline;" class=""><br class=""></span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; text-align: start; text-indent: 0px; text-transform: none; widows: 2; background-color: rgb(255, 255, 255); float: none; display: inline;" class="">Could you give me some detailed step-by-step instruction on how this original figure was prepared in chimera?</span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; text-align: start; text-indent: 0px; text-transform: none; widows: 2; background-color: rgb(255, 255, 255); float: none; display: inline;" class=""><br class=""></span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; text-align: start; text-indent: 0px; text-transform: none; widows: 2; background-color: rgb(255, 255, 255); float: none; display: inline;" class="">With many many thanks</span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; text-align: start; text-indent: 0px; text-transform: none; widows: 2; background-color: rgb(255, 255, 255); float: none; display: inline;" class=""><br class=""></span></div><div style="clear:both;" class=""><span style="font-family: Tahoma, Arial, STHeiti, SimSun; font-size: 14px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; text-align: start; text-indent: 0px; text-transform: none; widows: 2; background-color: rgb(255, 255, 255); float: none; display: inline;" class="">Yeping Sun  </span></div></div>_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></blockquote></div><br class=""></div></body></html>