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Re: [scipion-users] How to get a multi-color orientation distribution picture from Cryo-EF
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From: <pc...@cn...> - 2021-06-20 20:49:08
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<div dir='auto'>You're great! This is called fast response time!<div dir="auto"><br></div><div dir="auto">I actually didn't know there was a cryoEF plugin.</div><div dir="auto"><br></div><div dir="auto">🤦♂️</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 20 jun. 2021 15:22, Grigory Sharov <sha...@gm...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi again,<div><br /></div><div>I've added the color plot in the new cryoEF plugin release (3.0.12), which should be available in a few minutes.</div><div><br clear="all" /><div><div dir="ltr" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt">Best regards,<br />Grigory</span></font></div><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt"><br /></span></font></div><div style="color:rgb( 0 , 0 , 0 )"><font face="arial, helvetica, sans-serif" size="2"><span style="font-size:10pt">--------------------------------------------------------------------------------</span></font></div><div style="color:rgb( 0 , 0 , 0 )"><span style="font-size:12.8px">Grigory Sharov, Ph.D.</span><br style="font-size:12.8px" /><br style="font-size:12.8px" /><span style="font-size:12.8px">MRC Laboratory of Molecular Biology,</span><br style="font-size:12.8px" /><span style="font-size:12.8px">Francis Crick Avenue,</span><br style="font-size:12.8px" /><span style="font-size:12.8px">Cambridge Biomedical Campus,</span><br style="font-size:12.8px" /><span style="font-size:12.8px">Cambridge CB2 0QH, UK.</span><br style="font-size:12.8px" /><span style="font-size:12.8px">tel. </span><a href="tel:+44%201223%20267228" style="color:rgb( 17 , 85 , 204 );font-size:12.8px">+44 (0) 1223 267228</a></div><div style="color:rgb( 0 , 0 , 0 )"><span style="font-size:12.8px">e-mail: </span><a href="mailto:gsharov@mrc-lmb.cam.ac.uk" style="color:rgb( 17 , 85 , 204 );font-size:12.8px">gsharov@mrc-lmb.cam.ac.uk</a><br /></div></div></div></div></div></div></div></div></div></div></div></div></div><br /></div></div><br /><div class="elided-text"><div dir="ltr">On Fri, Jun 18, 2021 at 11:45 AM Pablo Conesa <<a href="mailto:pconesa@cnb.csic.es">pconesa@cnb.csic.es</a>> wrote:<br /></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"> <div> <p>Thanks! this is an interesting plot. Not yet available in Scipion, but I guess doable.<br /> </p> <div>On 18/6/21 10:10, 范宏成 wrote:<br /> </div> <blockquote> <div> <div> <div> <div style="font-family:'微软雅黑' , 'verdana' , 'microsoft yahei' , 'simsun' , sans-serif;line-height:22.4px;color:rgb( 49 , 53 , 59 )">Dear colleagues<span style="line-height:1.6">,</span></div> <div style="font-family:'微软雅黑' , 'verdana' , 'microsoft yahei' , 'simsun' , sans-serif;line-height:22.4px"><font style="color:rgb( 49 , 53 , 59 )" face="Arial"><span style="line-height:23.8px">I recently used the cryo-EF program in Scipion to try to quantify my protein's orientation distribution. I found it very useful compared to relion-orientation output and told me whether the preferential orientation influenced my protein's high resolution structure determination when using the single particle analysis. Recently, I found this paper <<</span></font><span style="color:rgb( 49 , 53 , 59 );font-family:'arial';line-height:23.8px">Multifunctional graphene supports for electron cryomicroscopy>>. The Figure3 ( </span><span style="color:rgb( 49 , 53 , 59 );font-family:'arial';line-height:1.7">Mapping the surface interaction profile of the 30S ribosomal subunit on a multifunctional graphene grid) was impressive. However, I found the cryoEF output was a single color picture ( see my result in the attachment, I already had the pdb model). I am curious about how to draw this multi-color picture (especially for the surface interaction site) based on the cryo-EF results . </span> <span style="color:rgb( 49 , 53 , 59 );font-family:'arial';line-height:1.7">I did't find this in the cryoEF output folder. Does anyone have some ideas or other programs in scipion which can help me find the preferential orientation site (euler angles values). Thank you! </span></div> <div style="font-family:'微软雅黑' , 'verdana' , 'microsoft yahei' , 'simsun' , sans-serif;line-height:22.4px;color:rgb( 49 , 53 , 59 )"><span style="line-height:1.7;font-family:'arial'">Best regards,</span></div> <div style="font-family:'微软雅黑' , 'verdana' , 'microsoft yahei' , 'simsun' , sans-serif;line-height:22.4px;color:rgb( 49 , 53 , 59 )"><font face="Arial"><span style="line-height:23.8px">Hongcheng Fan</span></font></div> </div> <div> <br /> </div> <div style="font-family:'微软雅黑'"> <div style="font-size:14px;padding:0px;margin:0px;line-height:14px"> <div style="padding-bottom:6px;margin-bottom:10px;border-bottom:1px solid rgb( 230 , 230 , 230 );display:inline-block"> <a href="https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=%E8%8C%83%E5%AE%8F%E6%88%90&uid=m18717124574%40163.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fsm9cc9cc9db2766bf0072c27595c17827b.jpg&items=%5B%22m18717124574%40163.com%22%5D" style="display:block;background:rgb( 255 , 255 , 255 );max-width:400px;padding:15px 0px 10px;text-decoration:none;outline:none"> <table style="width:100%;max-width:100%;table-layout:fixed;border-collapse:collapse;color:rgb( 155 , 158 , 161 );font-size:14px;line-height:1.3" cellpadding="0"><tbody><tr><td style="padding:0px;width:38px" width="38"> <img style="vertical-align:middle;width:38px;height:38px;border-radius:50%" src="https://mail-online.nosdn.127.net/sm9cc9cc9db2766bf0072c27595c17827b.jpg" width="38" height="38" /> </td><td style="padding:0px 0px 0px 10px;color:rgb( 49 , 53 , 59 )"> <div style="font-size:16px;font-weight:bold;width:100%;white-space:nowrap;text-overflow:ellipsis">范宏成</div> </td></tr><tr style="width:100%;font-size:14px"><td colspan="2" style="padding:10px 0px 0px;width:100%;font-size:14px"> <div style="width:100%;font-size:14px">m18717124574@163.com</div> </td></tr></tbody></table> </a> </div> </div> <div style="font-size:12px;color:rgb( 181 , 185 , 189 );line-height:18px"> 签名由 <a style="text-decoration:none;color:rgb( 65 , 150 , 255 );padding:0px 5px" href="https://mail.163.com/dashi/dlpro.html?from=mail81">网易邮箱大师</a> 定制 </div> </div> </div> </div> <br /> <fieldset></fieldset> <br /> <fieldset></fieldset> <pre>_______________________________________________ scipion-users mailing list <a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a> <a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a> </pre> </blockquote> <div>-- <br /> Pablo Conesa - <strong>Madrid <a href="http://scipion.i2pc.es">Scipion</a> team</strong></div> </div> _______________________________________________<br /> scipion-users mailing list<br /> <a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a><br /> <a href="https://lists.sourceforge.net/lists/listinfo/scipion-users">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><br /> </blockquote></div> </blockquote></div><br></div> |
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