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 [image: 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 > > ------------------------------ > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C24412f35c13142fe49dc08dc65265a9f%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638496462720640727%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=jcPNODLx5BJRvJt5UAQ99sMjWsY%2Bx7lil%2F6jF4rKxY8%3D&reserved=0> > > > Maria Håkansson, PhD, > Principal Scientist > > SARomics Biostructures AB > Medicon Village > SE-223 81 Lund, Sweden > > Mobile: +46 (0)76 8585706 > Web: www.saromics.com > > > > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C24412f35c13142fe49dc08dc65265a9f%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638496462720640727%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=jcPNODLx5BJRvJt5UAQ99sMjWsY%2Bx7lil%2F6jF4rKxY8%3D&reserved=0> > -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 ######################################################################## 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/
