've been updating our metadata to have info on the new residues I'm adding to gmml (Kdn/Kdo). I wrote a script that greps the glycam residue names from the latest prep file, then checks the old All_Residues.txt (list of glycam residue names in our metadata) for extra entries and adds them to the new All_Residues. It found these ones:
0Bc from old AllResidues file not found in new one. Adding it to the bottom.
3Bc from old AllResidues file not found in new one. Adding it to the bottom.
HYP from old AllResidues file not found in new one. Adding it to the bottom.
OLP from old AllResidues file not found in new one. Adding it to the bottom.
OLY from old AllResidues file not found in new one. Adding it to the bottom.
0bc from old AllResidues file not found in new one. Adding it to the bottom.
3bc from old AllResidues file not found in new one. Adding it to the bottom.
YAE from old AllResidues file not found in new one. Adding it to the bottom.
0Ae from old AllResidues file not found in new one. Adding it to the bottom.
2Ae from old AllResidues file not found in new one. Adding it to the bottom.
4Ae from old AllResidues file not found in new one. Adding it to the bottom.
YAe from old AllResidues file not found in new one. Adding it to the bottom.
So these are residues that we've added to the gmml metadata, but I don't have their prep entries ( prep entries contain templates that define 3d structure, charges and atom types for each of our residues). I believe the 0Bc, 0bc, 3bc and 3Bc are from the legacy builders ability to build Bac (click on the bacterial tab). We've lost that ability now unless I can find the prep files that were used.
I don't know where the Ae ones are from, or where their prep entries might be found.
HYP, OLP and OLY (O-linked Tyrosine) are for glycan-protein connections. No idea about prep files for those either.
've been updating our metadata to have info on the new residues I'm adding to gmml (Kdn/Kdo). I wrote a script that greps the glycam residue names from the latest prep file, then checks the old All_Residues.txt (list of glycam residue names in our metadata) for extra entries and adds them to the new All_Residues. It found these ones:
0Bc from old AllResidues file not found in new one. Adding it to the bottom. 3Bc from old AllResidues file not found in new one. Adding it to the bottom. HYP from old AllResidues file not found in new one. Adding it to the bottom. OLP from old AllResidues file not found in new one. Adding it to the bottom. OLY from old AllResidues file not found in new one. Adding it to the bottom. 0bc from old AllResidues file not found in new one. Adding it to the bottom. 3bc from old AllResidues file not found in new one. Adding it to the bottom. YAE from old AllResidues file not found in new one. Adding it to the bottom. 0Ae from old AllResidues file not found in new one. Adding it to the bottom. 2Ae from old AllResidues file not found in new one. Adding it to the bottom. 4Ae from old AllResidues file not found in new one. Adding it to the bottom. YAe from old AllResidues file not found in new one. Adding it to the bottom.
So these are residues that we've added to the gmml metadata, but I don't have their prep entries ( prep entries contain templates that define 3d structure, charges and atom types for each of our residues). I believe the 0Bc, 0bc, 3bc and 3Bc are from the legacy builders ability to build Bac (click on the bacterial tab). We've lost that ability now unless I can find the prep files that were used. I don't know where the Ae ones are from, or where their prep entries might be found. HYP, OLP and OLY (O-linked Tyrosine) are for glycan-protein connections. No idea about prep files for those either.