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

Oliver Grant olivercgrant at gmail.com
Wed Sep 6 01:34:53 PDT 2017


Hi Eric,

That's good with me, looking forward to hearing from you.

Best,

Oliver

On Wed, Sep 6, 2017 at 2:02 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
>
> 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> 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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