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glycoinfo / GlycanBuilder2

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Undetermined linkage bracket not vertically symmetric about reducing end... #20

Open edwardsnj opened 3 years ago

edwardsnj commented 3 years ago

This is more of a matter of taste, but I think the following structures would look better if the undetermined linkage bracket was symmetric about the horizontal axis defined by the reducing end monosaccharide.

Examples:

https://glymage.glyomics.org/image/snfg/extended/G00288RP.png https://glymage.glyomics.org/image/snfg/extended/G00249IY.png

Cases where non-symmetry look OK:

https://glymage.glyomics.org/image/snfg/extended/G00155YT.png https://glymage.glyomics.org/image/snfg/extended/G00247JV.png https://glymage.glyomics.org/image/snfg/extended/G00171RJ.png

ReneRanzinger commented 3 years ago

A bit of topic from symetric. But look at G00249IY. The GlycoCT does not say the Fuc is on one of the Gal. In fact it says the potential parent residue can be ANY monosaccharide of the core structure. Including the core-Fuc. So having the bracket across the entire structure makes sense. From the biological point of view only the two terminal Gal, the two GlcNAc before the Gal and the core GlcNAc are reasonable candidates. However, drawing tools like GWB did not allow to specify explicit parents (even thou GlycoCT and WURCS allow this). So most of these structures ended up with all residues being potential parents.

yamadaissaku commented 2 years ago

We have revised the undefined linkage bracket positions. image