I wrote something a while ago the finds an unused code. > % elbow.get_new_ligand_code
Unique ligand code : 7V8 > % elbow.get_new_ligand_code A Unique ligand code : A6E Cheers Nigel --- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov On Fri, Jun 5, 2015 at 6:59 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > > I use any 3 letter/number code that i want. If you read the corresponding > cif file into coot it is used in preference to any in the library. The PDB > deposition team will assign a code if it is a new ligand to the database. > Could you relay this to original poster? > > Thanks > > Jim Brannigan > > > On 5 June 2015 at 14:58, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > >> OK - thank you. >> How are things? >> E >> >> >> ---------- Forwarded message ---------- >> From: Jim Brannigan <jim.branni...@york.ac.uk> >> Date: 5 June 2015 at 14:39 >> Subject: Re: New ligand 3-letter code >> To: Eleanor Dodson <eleanor.dod...@york.ac.uk> >> >> >> Hi Eleanor >> >> I use any 3 letter/number code that i want. If you read the corresponding >> cif file into coot it is used in preference to any in the library. The PDB >> deposition team will assign a code if it is a new ligand to the database. >> Could you relay this to original poster? >> >> Thanks >> >> Jim Brannigan >> >> On 5 June 2015 at 11:28, Eleanor Dodson <eleanor.dod...@york.ac.uk> >> wrote: >> >>> I use your method - trial & error.. >>> It would be nice if at least there was a list somewhere of unassigned >>> codes! >>> >>> >>> On 5 June 2015 at 09:16, Lau Sze Yi (SIgN) < >>> lau_sze...@immunol.a-star.edu.sg> wrote: >>> >>>> Hi, >>>> >>>> What is the proper way of generating 3-letter code for a new ligand? As >>>> of now, I insert my ligand in Coot using smiles string and for the 3-letter >>>> code I picked a non-existent code by trial and error (not very efficient). >>>> A cif file with corresponding name which I generated using Phenix was >>>> imported into Coot. >>>> >>>> I am sure there is a proper way of doing this. Appreciate your feedback. >>>> >>>> Regards, >>>> Sze Yi >>>> >>> >>> >> >> >
