Thanks Eleanor for relaying my question from COOT and everyone that follows up
with the thread.
So this new ligand code search feature will be available in Phenix Gui? Look
forward to it.
Thanks,
Sze Yi
From: Nigel Moriarty nwmoria...@lbl.govmailto:nwmoria...@lbl.gov
Reply-To: Nigel Moriarty nwmoria...@lbl.govmailto:nwmoria...@lbl.gov
Date: Sunday, 7 June 2015 11:18 pm
To: CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] New ligand 3-letter code
Ed
Thanks for the feature request. I will be available in the next nightly build.
nigel% elbow.get_new_ligand_code A?3
Unique ligand code : AV3
Cheers
Nigel
---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.govmailto:nwmoria...@lbl.gov
Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.gov
On Sat, Jun 6, 2015 at 4:20 PM, Edward A. Berry
ber...@upstate.edumailto:ber...@upstate.edu wrote:
Neat! It's true the PDB will choose a unique code for you,
but they will use what you supply if it is already unique,
and it is nice to be able to choose something that can help
you remember what it stands for.
Gone are the days when we could choose meaningfull pdb ID's
(like 1PRC, 2PRC, 3PRC etc are all photosynthetic reaction center),
but there is still some freedom in choosing the ligand ID's.
They are filling up fast, though!
locust 123% elbow.get_new_ligand_code AC
Unique ligand code : AC3
locust 129% elbow.get_new_ligand_code A?3
Unique ligand code : A?3
eab
On 06/06/2015 12:13 PM, Nigel Moriarty wrote:
I wrote something a while ago the finds an unused code.
% elbow.get_new_ligand_code
Unique ligand code : 7V8
% elbow.get_new_ligand_code A
Unique ligand code : A6E
Cheers
Nigel
---
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709tel:510-486-5709 Email :
nwmoria...@lbl.govmailto:nwmoria...@lbl.gov
Fax : 510-486-5909tel:510-486-5909 Web :
CCI.LBL.govhttp://CCI.LBL.gov http://CCI.LBL.gov
On Fri, Jun 5, 2015 at 6:59 AM, Eleanor Dodson
eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk
mailto:eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk wrote:
I use any 3 letter/number code that i want. If you read the corresponding
cif file into coot it is used in preference to any in the library. The PDB
deposition team will assign a code if it is a new ligand to the database. Could
you relay this to original poster?
Thanks
Jim Brannigan
On 5 June 2015 at 14:58, Eleanor Dodson
eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk
mailto:eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk wrote:
OK - thank you.
How are things?
E
-- Forwarded message --
From: *Jim Brannigan*
jim.branni...@york.ac.ukmailto:jim.branni...@york.ac.uk
mailto:jim.branni...@york.ac.ukmailto:jim.branni...@york.ac.uk
Date: 5 June 2015 at 14:39
Subject: Re: New ligand 3-letter code
To: Eleanor Dodson
eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk
mailto:eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk
Hi Eleanor
I use any 3 letter/number code that i want. If you read the
corresponding cif file into coot it is used in preference to any in the
library. The PDB deposition team will assign a code if it is a new ligand to
the database. Could you relay this to original poster?
Thanks
Jim Brannigan
On 5 June 2015 at 11:28, Eleanor Dodson
eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk
mailto:eleanor.dod...@york.ac.ukmailto:eleanor.dod...@york.ac.uk wrote:
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.sgmailto:lau_sze...@immunol.a-star.edu.sg
mailto:lau_sze...@immunol.a-star.edu.sgmailto: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
