Re: [chimerax-users] [Chimera-users] 3D-SNFG symbol representation for carbohydrate molecules
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@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@gmail.com mailto:olivercgrant@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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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@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@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@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.
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
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participants (2)
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Eric Pettersen -
Oliver Grant