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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