[Chimera-users] 3D-SNFG symbol representation for carbohydrate molecules

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 5 17:02:11 PDT 2017

Hi Oliver,
	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.
	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. :-)


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 31, 2017, at 4:22 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Dear Dr. Grant,
> 	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.
> —Eric
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
>> On Aug 31, 2017, at 7:18 AM, Oliver Grant <olivercgrant at gmail.com <mailto:olivercgrant at gmail.com>> wrote:
>> Dear developers,
>> The carbohydrate community has decided on a standard symbol representation for carbohydrates. The article is here <https://academic.oup.com/glycob/article-lookup/doi/10.1093/glycob/cwv091>, and the webpage is here <https://www.ncbi.nlm.nih.gov/books/NBK310273/>. Our group has created a 3D version <http://glycam.org/docs/othertoolsservice/2016/06/03/3d-symbol-nomenclature-for-glycans-3d-snfg/> of the symbols within the software VMD. Here's a video showing both versions. <http://glycam.org/docs/othertoolsservice/wp-content/uploads/sites/15/2016/06/3D-SNG_PDB-3SGJ.mp4> We have also worked with David Sehnal to implement this into LiteMol, here is an example <https://webchemdev.ncbr.muni.cz/LiteMol/Viewer/?loadFromCS=5a6z>. I wanted to reach out and see if you are interested to implement this representation within Chimera? We can discuss the details if so.
>> Regards,
>> Dr. Oliver Grant
>> Associate Research Scientist
>> Complex Carbohydrate Research Center
>> Athens, GA, USA.
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