Dear Stefanie, We routinely use DRG or LIG or numbers in running refmac and do not see the issue. Maybe check if .cif and .pdb file has the same code for the compound and also, if the issue is not coming from other molecule in the structure?
Another option would to be try a different computer to make sure that it is not related to your ccp4 installation. Best regards Cyprian Cyprian Cukier, Ph.D. Head of Structural Biology Selvita S.A. From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Garib Murshudov Sent: Friday, April 26, 2024 1:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] add ligand with AceDRG CAUTION: External Sender. Please do not click on links or open attachments from senders you do not trust. Refmac by itself should not care about duplicated residue names in the monomer library. It takes the last monomer. There should be something on the interface preventing this. Longer than three letters should be available from the next release of ccp4. New acedrg and Refmacat should be able to deal with them. Ccp4i2 might not be ready. Regards Garib On 26 Apr 2024, at 11:21, FREITAG-POHL, STEFANIE <stefanie.freitag-p...@durham.ac.uk<mailto: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 ######################################################################## 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/
