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The PDB has always let me keep my three-letter codes if they were unclaimed IDs. For example, I had a series of drugs from a South African collaborator during the South African World Cup, and I named all the ligands VZ# for the stupid vuvuzelas that were blaring in the background while I was trying to refine the structures. The PDB let me keep all the IDs except for the one that was published previously. Unless there has been a policy change recently, I don't think there is an issue with keeping the unclaimed ID you give it. Cheers, Katherine On Tue, Jun 23, 2015 at 5:31 AM, Paul Emsley <[log in to unmask]> wrote: > > It seems to me that Rachel's answer is somewhat unclear. To rephrase > then: if I deposit a new structure with a new ligand and I give it an > as-yet-unassigned three-letter-code, will the RCSB/wwPDB keep the code I > gave it? Actually a straight reading of Rachel's answer is "no" - but I > understood the opposite to be the case (which is why I wrote > coot.available-comp-id). > > Paul. > > > > On 19/06/2015 20:49, Sheriff, Steven wrote: > > 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:[log in to unmask] > <[log in to unmask]>] > *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 > > [log in to unmask] > > > > *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:[log in to unmask] <[log in to unmask]>] *On Behalf Of *Eleanor > Dodson > *Sent:* Friday, June 05, 2015 6:28 AM > *To:* [log in to unmask] > *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) < > [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 > > > ------------------------------ > > 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. > > > -- "Nil illegitimo carborundum"* - *Didactylos