Dear Marion, If you read in your corrected .cif file in Coot or your refinement program, it will override the (default) CCP4 .cif file. You can also correct the installed CCP4 .cif file. I once did this. However, these changes are lost when you update the CCP4 installation, so best is to ask the CCP4 developers do correct their .cif file.
Best, Herman Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Marion Schuller Gesendet: Samstag, 17. September 2022 16:48 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Help with isomer ligand from PDB database Dear CCP4bb community, I am writing regarding a problem with the refinement of an isomer ligand. I try to refine a structure which has the ligand "Carba-NAD" (as beta isomer) bound. This ligand is already in the pdb database as "CNA". Although the ligand is in its beta-Carba-NAD form in the database, it is loaded into WinCoot as alpha isomer. When generating the restraints of Carba-NAD (via the grade server, calling it also "CNA"), I can load and refine the correct beta isomer ligand as long as I provide the grade-generated .cif file otherwise it would refine it back to the alpha isomer. Yet, in the preliminary preparation of the wwPDB X-ray validation report for structure deposition, the message flags up that the ligand "could not be matched to an existing wwPDB Chemical Component Dictionary definition". With an older ccp4 version in the background, I noticed that WinCoot would however load the beta isomer and I am now wondering if this problem lies in the .cif file of the new ccp4 library. Is there a possibility to check/correct the CNA file in the current ccp4 library or would there be a different way for solving this problem? I would be very grateful for support and help! With kind regards and many thanks in advance, Marion ________________________________ 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://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/
