I'm not aware that anything has changed since the last time this was discussed on the BB. Currently there is no ideal solution since even the mmCIF PDB format does not allow a proper description of the situation of atoms whose position cannot be placed due to the absence of data.
The "Ligand Validation workshop" produced recommendations (Structure, 2016, 24(4), 502-508) that included the addition of a flag to atomic properties that indicates that the atom's position was generated w/o experimental guidance. To my knowledge this has not be done. In the absence of this solution we can only repeat the, conflicting, arguments in favor or against the various less than optimal solutions. You can go back to the archives to find those. Dale Tronrud On 4/28/2020 8:37 AM, Thomas, Leonard M. wrote: > Hello all, > > This is one of those issues that seems to come up now and then. I have > been working on a structure that obviously has some radiation damage as > indicted by negative density and/or high thermal parameters. Since we > know that residue X is in the sequence the sidechain should be there and > is just flopping around or has been damaged/removed by radiation > exposure. My questions is what is the current thinking on presenting > these residues for deposition. Remove the side chain atoms, drop the > occupancy to zero, just let them behave as they want ie high B factors > some negative density. > > Cheers, > Len > > Leonard Thomas > lmtho...@ou.edu <mailto:lmtho...@ou.edu> > > > > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
