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: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
<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
<https://twitter.com/#%21/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
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