Dear Oliver and CCP4BB readers, This obsoleted LIG came from PDB entry 1JVP deposited in 2001 by Jean-Michel Rondeau working at Novartis. He must simply have been the first person to deposit a structure in which the ligand was called LIG ... . That molecule is now called 89E, but as Phil showed, there are still remnants of its old identity.
Best wishes, Gerard. -- On Fri, Apr 26, 2024 at 04:31:13PM +0100, Oliver Smart wrote: > Hi Stefanie, > > If you want to try Grade2 (for a non-confidential ligand) then this is easy > to do using the Grade Web Server > > https://grade.globalphasing.org/ > > We have altered our default "3-letter code” (aka PDB chemical component ID) > to “LIG”. > The reserved PDB two letter codes 01 to 99 are also fine (as are INH and > DRG). > We understand from users that Grade2 restraint dictionaries work well with > REFMAC (as to AceDG) > Checking my installation of CCP4 8.0 there are no distributed dictionaries > for LIG, DRG or 01 to 99. > > There was a PDB component LIG that was obsoleted in 2021 > https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/LIG.cif > And there was a restraint dictionary for this distributed with CCP4 7.0. > > Perhaps you are picking up things from an old CCP4 installation > > Hope this helps, > > Oliver > > > > > > On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE > > <stefanie.freitag-p...@durham.ac.uk> wrote: > > > > Dear all, > > > > thank you so much for all your suggestions. > > > > Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is > > complaining that there is a clash with an already existing ligand (even > > DRG, LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters. > > > > I am not quite sure how to bypass this issue as I think Refmac is also > > insisting on 3-letters for ligands (???) > > > > I have not tried Grade yet. > > > > Any advise much appreciated. > > > > 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 > > <mailto:stefanie.freitag-p...@durham.ac.uk> > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK > > <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of FREITAG-POHL, STEFANIE > > <stefanie.freitag-p...@durham.ac.uk > > <mailto:stefanie.freitag-p...@durham.ac.uk>> > > Sent: 25 April 2024 13:01 > > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > > <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> > > Subject: [ccp4bb] add ligand with AceDRG > > > > [EXTERNAL EMAIL] > > 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 > > <mailto:stefanie.freitag-p...@durham.ac.uk> > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
