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MonomerLibrary / monomers

dictionary of monomers and links
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new group for phosphorothioate DNA #53

Open keitaroyam opened 5 months ago

keitaroyam commented 5 months ago

Phosphorothioate DNA is a modified DNA where the OP2 atom is substituted with sulfur (S2P); for example: AS PST GS SC. I would like to have a new group for this kind of monomers, to make refinement easier.

There are some inconsistencies in the CCD. In AS, there is P=S double bond, while in GS it's P-SH single bond. I fixed P-SH type monomers: 1SC 48Z 6NW 6OO C7R C7S DV3 F2T G46 GS OKN OKQ OKT U37 YA4. Hopefully CCD will accept these fixes (haven't ask yet).

I don't know if "S-NA" is a good name - should it be "SDNA/RNA", or any alternative? We can proceed once we decide a name for this new group.

GaribMurshudov commented 5 months ago

I think SDNA/SRNA would be workable

keitaroyam commented 5 months ago

Do you mean SDNA/RNA? SDNA/SRNA is too wide (9 letters) and Refmac cannot handle it (and won't fit the PDB format).

GaribMurshudov commented 5 months ago

Ok. Then you can have: SDNA/RNA, you could also have SDNA, SRNA (I think current CCD has these)

keitaroyam commented 5 months ago

Yes, but we don't need to separate them, unless we need a link around O2'.

For now we do have DNA, RNA and DNA/RNA. This is a bit confusing..

GaribMurshudov commented 5 months ago

I understand. Unless in the current mechanism we remove RNA and DNA, keep only RNA/DNA you could also have the same mechanism for SDNA and SRNA

GaribMurshudov commented 3 months ago

What is happening with this addition?

keitaroyam commented 3 months ago

I just need to find time to finalise this