Dear all, We also have had problems with FAD, FMN and I think NAD when depositing to the PDB. The ligand checks in PDB were expecting values different for some bonds and angles and our values either corresponded to the CCP4 dictionaries (and/or) to our defined values where there were modifications, always taken from the CSD average values and checked against similar situations found in the CCP4 dictionaries.
I.e. we left the "raised flags" in the PDB without much attention as we assumed that for some reasons the geometrical values being used there are not what CCP4 and we are convinced would be the right ones. Now, Jan's question triggered mine .. Anybody else had similar experience with such ligands? Jan Dohnalek On Fri, Jul 29, 2022 at 11:54 AM Jan Stransky <[email protected]> wrote: > Hi all, > > while validating X-ray structure using Molprobity (web service), we got > systematic outlier flags on CE1-NE2 distance in histidines. The distance > is 1.36A. > > I have tested it also using high resolution lysozyme structure, I have > laying around. There the distance refines as 1.31A and Molprobity is > happy, but when Bong Angels are called in Coot (Regularize zone button > :-)) the bond length goes to 1.36A and Molprobity is unhappy again. > > So I would like to ask, who is right or where else the problem can be. > > Best regards, > > Jan > > P.S. CCP4 is version 8.0.002 > > ######################################################################## > > 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/ > -- Jan Dohnalek, Ph.D Institute of Biotechnology Academy of Sciences of the Czech Republic Biocev Prumyslova 595 252 50 Vestec near Prague Czech Republic Tel. +420 325 873 758 ######################################################################## 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/
