All: Since the original query was cross-posted on both the COOT mailing list and the CCP4BB Rachel Green gave me permission to forward this to both. She provides links about the mechanism of assignment of 3-letter codes. In the third link below, my original suggestion to the COOT mailing list that one could just use UNK is incorrect as that is reserved for unknown amino acids. According to this document, I should have suggested UNL for an unknown ligand.
Steven From: Rachel Kramer Green [mailto:kra...@rcsb.rutgers.edu] Sent: Tuesday, June 16, 2015 10:21 AM To: Sheriff, Steven Cc: info Subject: Re: New ligand 3-letter code (help-7071) Dear Steven, During annotation of ligands, all chemical components present in the structure are compared against the definitions in the Chemical Component Dictionary (http://www.wwpdb.org/data/ccd). If the ligand is not in the dictionary, a three letter code is assigned. See http://www.wwpdb.org/documentation/policy#toc_assignment. In the future, a group of three-letter codes may be set aside to be used during refinement to flag new ligands. Clarification about the ligand ids assignment and in particular the usage of UNX/UNL/UNK residues can be found at http://www.wwpdb.org/documentation/procedure#toc_2. Best wishes, Rachel ________________________________ Rachel Kramer Green, Ph.D. RCSB PDB kra...@rcsb.rutgers.edu<mailto:kra...@rcsb.rutgers.edu> New! Deposit X-ray data with the wwPDB at: http://deposit.wwpdb.org/deposition (NMR and 3DEM coming soon). ___________________________________________________________ Twitter: https://twitter.com/#!/buildmodels Facebook: http://www.facebook.com/RCSBPDB On 6/5/2015 7:50 AM, Sheriff, Steven wrote: All: Why the concern for unassigned three-letter codes? The wwPDB isn’t going to let you assign a three-letter code, it will choose its own code. At BMS (a pharmaceutical company), we do many hundreds of structures a year with ligands and we assign the same, already assigned, three-letter code for all of our ligands (unless we have two or more different ligands in a single structure, in which case we use two or more different already assigned three-letter codes). COOT can mostly handle this. However, I believe that if you want an unassigned code, the wwPDB has set aside UNK[nown] for this purpose. Steven From: Mailing list for users of COOT Crystallographic Software [mailto:COOT@JISCMAIL.AC.UK] On Behalf Of Eleanor Dodson Sent: Friday, June 05, 2015 6:28 AM To: COOT@JISCMAIL.AC.UK<mailto:COOT@JISCMAIL.AC.UK> Subject: Re: New ligand 3-letter code 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 ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited. ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
