Hotfixes sphingomyelin and others

[comcon1]

Some just-found mistakes

[comcon1]

Problems has been found with pure SM systems.

[tfmFerreira]

The stereospecific numbering (sn) is well defined for the glycerol-backbone of glycero lipids. But I am not sure if there is a well defined equivalent for sphingolipids. Did you already think of this? I will check in Marsh's textbook.

[comcon1]

The stereospecific numbering (sn) is well defined for the glycerol-backbone of glycero lipids. But I am not sure if there is a well defined equivalent for sphingolipids. Did you already think of this? I will check in Marsh's textbook.

I would name the side chain "sn-2" because it's branched up higher from the backbone. Stereonumbering is related to glycerol L and R forms. This is an agreement how to number glycerol, where is 1 and 3. For pure glycerol 1 and 3 are the same but for substituted there is an agreement. In sphingomyelin, we don't have it, but it's meaningful to compare N side-chain with sn-2 and not sn-1. So, I would flip fragment marks.

[comcon1]

For glycerolipids, you have archaeal lipids where glycerol have different stereochemestry and then FA are named as sn-2 and sn-3. So that makes sense to name it "sn" . For sphingomyelin, there is no difference in nature of sphingosine. And the numeration is always the same because even if you synthesize stereodifferent sphingosine, the headgroup will be always at position 1. We can issue this clarification in the specific documentation page and rename chains accordingly. Do you want me to rename chains? That will affect quality files a bit.

[markussmiettinen]

I do not have a strong opinion here. My five cents would be that it is a bit misleading to call the sphingo-tails sn-X, and if there is another existing naming convention (e.g. in Marsh's book that @tfmFerreira planned to check out), then we should go for that. But I am also fine with having them sn-X, if this is clearly documented.