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:[email protected]] On Behalf Of Eleanor Dodson Sent: Friday, June 05, 2015 6:28 AM To: [email protected] 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) <[email protected]<mailto:[email protected]>> 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.
