 |
 |
One thing to beware of is that of course un-released structures may have the code that you choose - structures can be on hold for over a year (the rules say a year but in practice release is often slower) and any new ligands and codes with them. Ligand codes are assigned at deposition and the description stored privately in a wwPDB database I believe. So your ligand code may be already there but not visible until it is copied into the public Chemical Component Dictionary at the time of release. Conversely your 'new' ligand _structure_ may be in an un-released entry deposited by some other crystallographer and already assigned a 3-letter code. So your choice will be overwritten at deposition in any case. This produces a problem when multiple competing groups deposit structures containing the same novel ligand. As the database will not expect duplicates, only the first depositor will get assigned a new 3-letter code. However then there should be alarm bells for the second depositor if their 'novel' ligand turns out to have a pre-existing three letter code! I suspect there must have been cases where this happened but was not spotted by the depositors. But if it happens to you then maybe it's time to speed up publication... I don't know if it has happened that one crystallographer has 'hastened' the release of the ligand description of another worker by publishing it in complex with a solved macromolecule. Perhaps the clever people at the PDB do a switch at the last minute? Best wishes, Martyn Martyn Symmons Cambridge On Mon, Jun 8, 2015 at 3:12 AM, Lau Sze Yi (SIgN) < [log in to unmask]> wrote: > 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 <[log in to unmask]> > Reply-To: Nigel Moriarty <[log in to unmask]> > Date: Sunday, 7 June 2015 11:18 pm > To: "[log in to unmask]" <[log in to unmask]> > 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 : [log in to unmask] > Fax : 510-486-5909 Web : CCI.LBL.gov > > On Sat, Jun 6, 2015 at 4:20 PM, Edward A. Berry <[log in to unmask]> > 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 : [log in to unmask] >>> Fax : 510-486-5909 Web : CCI.LBL.gov <http://CCI.LBL.gov> >>> >>> On Fri, Jun 5, 2015 at 6:59 AM, Eleanor Dodson < >>> [log in to unmask] <mailto:[log in to unmask]>> 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 <[log in to unmask] >>> <mailto:[log in to unmask]>> wrote: >>> >>> OK - thank you. >>> How are things? >>> E >>> >>> >>> ---------- Forwarded message ---------- >>> From: *Jim Brannigan* <[log in to unmask] <mailto: >>> [log in to unmask]>> >>> Date: 5 June 2015 at 14:39 >>> Subject: Re: New ligand 3-letter code >>> To: Eleanor Dodson <[log in to unmask] <mailto: >>> [log in to unmask]>> >>> >>> >>> 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 < >>> [log in to unmask] <mailto:[log in to unmask]>> 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) < >>> [log in to unmask] <mailto: >>> [log in to unmask]>> 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 >>> >>> >>> >>> >>> >>> >>> >