<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 Oliver,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>We discussed this at the meeting today and the upshot is that we are very interested in doing this, but it will take us awhile to get to it. We intend to make a beta release of ChimeraX by the end of the year and there’s a lot of work to get done between then and now. Part of that work is to implement the “Nucleotides” representation that you see in regular Chimera but that isn’t yet available in ChimeraX. The “alternative atom depiction” that Nucleotides provides requires much of the same underlying support that showing the alternative carbohydrate depictions will require. Implementing Nucleotides first will allow us to iron out the issues involved in supplying that support and debug it. That will make implementing the 3D-SNFG representation much faster and improve its reliability. So we hope to be able to provide the carbohydrate depictions not long after the beta release date.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>I’d like to provide something faster, but as a practical matter I think this is the best we can do. I’m sure we will have questions about the details once we get onto the implementation, and hope you won’t mind if need to bug you a bit. :-)</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); 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=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div><br class=""></div><div><blockquote type="cite" class=""><div class="">On Aug 31, 2017, at 4:22 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>> 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="">Dear Dr. Grant,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>We are definitely interested, though we would be more likely to implement it in ChimeraX than Chimera, since most of our new work is in ChimeraX and also ChimeraX has better underlying support for adding new depictions like this. We will discuss this in a meeting on Tuesday and get back to you with further details.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; 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=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div></div>
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<br class=""><div class=""><blockquote type="cite" class=""><div class="">On Aug 31, 2017, at 7:18 AM, Oliver Grant <<a href="mailto:olivercgrant@gmail.com" class="">olivercgrant@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Dear developers,<div class=""><br class=""></div><div class=""><div style="font-size:12.8px" class="">The <span class="gmail-il">carbohydrate</span> community has decided on a standard symbol representation for <span class="gmail-il">carbohydrates</span>. The <a href="https://academic.oup.com/glycob/article-lookup/doi/10.1093/glycob/cwv091" target="_blank" class="">article is here</a>, and the webpage is <a href="https://www.ncbi.nlm.nih.gov/books/NBK310273/" target="_blank" class="">here</a>. Our group has created a <a href="http://glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-for-glycans-3d-snfg/" target="_blank" class="">3D version</a> of the symbols within the software VMD. Here's a <a href="http://glycam.org/docs/othertoolsservice/wp-content/uploads/sites/15/2016/06/3D-SNG_PDB-3SGJ.mp4" target="_blank" class="">video showing both versions.</a> We have also worked with David Sehnal to implement this into LiteMol, <a href="https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/?loadFromCS=5a6z" target="_blank" class="">here is an example</a>. I wanted to reach out and see if you are interested to implement this representation within Chimera? We can discuss the details if so.</div><div style="font-size:12.8px" class=""><br class=""></div><div style="font-size:12.8px" class="">Regards,</div><div style="font-size:12.8px" class=""><br clear="all" class=""><div class=""><div class="gmail-m_7688135063445531719m_1610079294999341939m_-621303809887641571gmail-m_557726968742856769m_-2689295291951976641gmail_signature"><div dir="ltr" class=""><div class=""><font face="arial, helvetica, sans-serif" class="">Dr. Oliver Grant</font></div><div class=""><font face="arial, helvetica, sans-serif" class="">Associate Research Scientist</font></div><div class=""><span style="font-family:arial,helvetica,sans-serif" class="">Complex <span class="gmail-il">Carbohydrate</span> Research Center</span><br class=""></div><div class=""><font face="arial, helvetica, sans-serif" class="">Athens, GA, USA.</font></div></div></div></div></div><div class=""><div class=""><div class="gmail-m_-2600699859382478649gmail_signature"><div dir="ltr" class=""><br class=""></div></div></div>
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