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/
