The PDB format does not encode the bond orders (single, double, triple, aromatic bond) that are required to produce the correct format of input (SMILES / MOL / SDF / MOL2 / mmCIF) to Grade. This is particularly important if some or all H atoms are absent and/or the PDB co-ordinates have not been refined, as then the bond orders and H atom placement cannot always be reliably determined.
I've seen several cases where the PDB automated deposition has placed H atoms incorrectly in a ligand and shown an incorrect chemical structure diagram even where the ligand has undergone refinement. Ideally of course it's up to the depositor to supply SMILES for new ligands to eliminate all doubt (this may now be a requirement). This is particularly a problem in the case of covalently-bound ligands because the bonding may differ between the free and bound ligands. The depositor will usually supply the SMILES for the free ligand but obviously one cannot assume the same bond orders and H atom placement for the bound ligand. For this reason the restraint dictionaries actually used in the refinement should always be supplied (this also makes validation much easier). Cheers -- Ian On Fri, 19 May 2023, 17:11 Tim Gruene, <tim.gru...@univie.ac.at> wrote: > Hi Frank, > > in line with Paul's comment, what is so apparent about openbabel not > doing the job? I use it frequently to generate the input from PDB to the > Grade-Server. > > Cheers, > Tim > > On Fri, 19 May 2023 10:28:32 +0100 Frank von Delft > <frank.vonde...@cmd.ox.ac.uk> wrote: > > > OpenBabel apparently does not. > > > -- > -- > Tim Gruene > Head of the Centre for X-ray Structure Analysis > Faculty of Chemistry > University of Vienna > > Phone: +43-1-4277-70202 > > GPG Key ID = A46BEE1A > > ######################################################################## > > 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/ > ######################################################################## 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/
