<div dir="ltr">Hi Eric,<div><br></div><div>That's good with me, looking forward to hearing from you.</div><div><br></div><div>Best,</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div><font face="arial, helvetica, sans-serif">Oliver</font></div></div></div></div></div>
<br><div class="gmail_quote">On Wed, Sep 6, 2017 at 2:02 AM, Eric Pettersen <span dir="ltr"><<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Oliver,<div><span class="m_-4455810140153293592Apple-tab-span" style="white-space:pre-wrap"> </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><span class="m_-4455810140153293592Apple-tab-span" style="white-space:pre-wrap"> </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><span class="HOEnZb"><font color="#888888"><div><br></div><div>—Eric</div></font></span><div><span class=""><br><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div><span class="m_-4455810140153293592Apple-tab-span" style="white-space:pre-wrap"> </span>Eric Pettersen</div><div><span class="m_-4455810140153293592Apple-tab-span" style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div><div><br></div></div><br></div></span><div><div class="h5"><div><blockquote type="cite"><div>On Aug 31, 2017, at 4:22 PM, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" target="_blank">pett@cgl.ucsf.edu</a>> wrote:</div><br class="m_-4455810140153293592Apple-interchange-newline"><div><div style="word-wrap:break-word">Dear Dr. Grant,<div><span class="m_-4455810140153293592Apple-tab-span" style="white-space:pre-wrap"> </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><br></div><div>—Eric</div><div><br><div>
<div style="letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div><span class="m_-4455810140153293592Apple-tab-span" style="white-space:pre-wrap"> </span>Eric Pettersen</div><div><span class="m_-4455810140153293592Apple-tab-span" style="white-space:pre-wrap"> </span>UCSF Computer Graphics Lab</div></div>
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<br><div><blockquote type="cite"><div>On Aug 31, 2017, at 7:18 AM, Oliver Grant <<a href="mailto:olivercgrant@gmail.com" target="_blank">olivercgrant@gmail.com</a>> wrote:</div><br class="m_-4455810140153293592Apple-interchange-newline"><div><div dir="ltr">Dear developers,<div><br></div><div><div style="font-size:12.8px">The <span class="m_-4455810140153293592gmail-il">carbohydrate</span> community has decided on a standard symbol representation for <span class="m_-4455810140153293592gmail-il">carbohydrates</span>. The <a href="https://academic.oup.com/glycob/article-lookup/doi/10.1093/glycob/cwv091" target="_blank">article is here</a>, and the webpage is <a href="https://www.ncbi.nlm.nih.gov/books/NBK310273/" target="_blank">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">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">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">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"><br></div><div style="font-size:12.8px">Regards,</div><div style="font-size:12.8px"><br clear="all"><div><div class="m_-4455810140153293592gmail-m_7688135063445531719m_1610079294999341939m_-621303809887641571gmail-m_557726968742856769m_-2689295291951976641gmail_signature"><div dir="ltr"><div><font face="arial, helvetica, sans-serif">Dr. Oliver Grant</font></div><div><font face="arial, helvetica, sans-serif">Associate Research Scientist</font></div><div><span style="font-family:arial,helvetica,sans-serif">Complex <span class="m_-4455810140153293592gmail-il">Carbohydrate</span> Research Center</span><br></div><div><font face="arial, helvetica, sans-serif">Athens, GA, USA.</font></div></div></div></div></div><div><div><div class="m_-4455810140153293592gmail-m_-2600699859382478649gmail_signature"><div dir="ltr"><br></div></div></div>
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