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

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

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]] 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

 

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