Thanks Eleanor for relaying my question from COOT and everyone that follows up with the thread.
So this new ligand code search feature will be available in Phenix Gui? Look forward to it. Thanks, Sze Yi From: Nigel Moriarty <nwmoria...@lbl.gov<mailto:nwmoria...@lbl.gov>> Reply-To: Nigel Moriarty <nwmoria...@lbl.gov<mailto:nwmoria...@lbl.gov>> Date: Sunday, 7 June 2015 11:18 pm To: "CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>" <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: Re: [ccp4bb] New ligand 3-letter code 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<mailto:nwmoria...@lbl.gov> Fax : 510-486-5909 Web : CCI.LBL.gov<http://CCI.LBL.gov> On Sat, Jun 6, 2015 at 4:20 PM, Edward A. Berry <ber...@upstate.edu<mailto: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<tel:510-486-5709> Email : nwmoria...@lbl.gov<mailto:nwmoria...@lbl.gov> Fax : 510-486-5909<tel:510-486-5909> Web : CCI.LBL.gov<http://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> <mailto: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> <mailto: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> <mailto: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> <mailto: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> <mailto: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> <mailto: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
