Hi Diana,
Could you please clarify where you are searching?
LIG is obsolete and definitely not in use.
Cheers,
Deborah
On 26/04/2024 15:40, Diana Tomchick wrote:
But I think that is a mistake, if you search for LIG in the PDB, it
brings up a definite ligand that has that 3-letter code.
Diana
Sent from my iPhone
On Apr 26, 2024, at 8:04 AM, Deborah Harrus <dhar...@ebi.ac.uk> wrote:
Dear all,
Just to clarify, "LIG" is also a reserved code, so it's safe to use.
See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6
Kind regards,
Deborah Harrus
PDBe
On 25/04/2024 16:04, Diana Tomchick wrote:
The PDB has reserved the following codes for unknown ligands:
DRG
INH
01 - 99
Using one of these should not cause you the described problems. I
successfully used
99
just last week. If you try to use
999 or LIG
these will not work, there are ligands assigned to those codes.
Diana
Sent from my iPhone
On Apr 25, 2024, at 8:03 AM, Nicholas Clark
<0000b2b1c7e93c2d-dmarc-requ...@jiscmail.ac.uk> wrote:
EXTERNAL MAIL
Hi Stefanie,
Why can you only use "taken" three letter codes? In the "output
monomer" box, you should be able to enter whatever you'd like for
the "Three letter code for output monomer". In the attached image,
this is shown as "DRG" but can be changed to any 3 letter code of
your choice. Obviously, just make sure your existing selection does
not exist in the PDB.
Best,
Nick Clark
<AdeDRG_jobwindow.png>
On Thu, Apr 25, 2024 at 8:51 AM Maria Håkansson
<maria.hakans...@saromics.com> wrote:
Hi Stefanie,
Can you manually edit the restraints file using TextEdit and
find and replace and the pdb
file of course?
Other option is to use Grade or Grade2 and the smiles string if
you have this software installed.
I often find this easier than ccp4i2.
Best regards and good luck!
Maria
On 25 Apr 2024, at 14:01, FREITAG-POHL, STEFANIE
<stefanie.freitag-p...@durham.ac.uk> wrote:
Hi all,
I have trouble adding a ligand with AceDRG in CCP4i2 into my
refinement:
I put in a smilesstring and the ligand is written ok, but
since I can only chose already 'taken' 3-letter-codes the
refinement always crashes as there is a clash with existing
library entries.
Is there any way around this? How do I add a novel ligand?
Thanks so much for your help.
Best wishes,
Stefanie
Dr. Stefanie Freitag-Pohl (she/her)
Durham University
Department of Chemistry
South Road, Durham
DH1 3LE
United Kingdom
0191 334 2596
stefanie.freitag-p...@durham.ac.uk
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