Ed Thanks for the feature request. I will be available in the next nightly build.
nigel% elbow.get_new_ligand_code "A?3" Unique ligand code : AV3 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 Sat, Jun 6, 2015 at 4:20 PM, Edward A. Berry <ber...@upstate.edu> wrote: > Neat! It's true the PDB will choose a unique code for you, > but they will use what you supply if it is already unique, > and it is nice to be able to choose something that can help > you remember what it stands for. > Gone are the days when we could choose meaningfull pdb ID's > (like 1PRC, 2PRC, 3PRC etc are all photosynthetic reaction center), > but there is still some freedom in choosing the ligand ID's. > They are filling up fast, though! > > locust 123% elbow.get_new_ligand_code AC > Unique ligand code : AC3 > > locust 129% elbow.get_new_ligand_code "A?3" > Unique ligand code : A?3 > > eab > > On 06/06/2015 12:13 PM, Nigel Moriarty wrote: > >> 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 <http://CCI.LBL.gov> >> >> On Fri, Jun 5, 2015 at 6:59 AM, Eleanor Dodson <eleanor.dod...@york.ac.uk >> <mailto: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 >> <mailto:eleanor.dod...@york.ac.uk>> wrote: >> >> OK - thank you. >> How are things? >> E >> >> >> ---------- Forwarded message ---------- >> From: *Jim Brannigan* <jim.branni...@york.ac.uk <mailto: >> 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 <mailto: >> 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 <mailto: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 <mailto: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 >> >> >> >> >> >> >>
