Dear all, to trim or not to to trim….
- what is the difference between highly disordered side-chain atoms versus disordered bulk-solvent atoms? Do not both represent a continuum function with a comparable electron-density distribution? Have not solvent and side-chain atoms merged/mixed at this position in space and with this, are effectively indistinguishable (contrast loss i.e. similar contribution to diffraction) from one another? - are current solvent models comprehensive enough in that modelling of atoms with very high B factors is really mutually beneficial for bulk and structure model? - is model bias (overfitting) not increased by modelling highly disordered side-chain atoms (Rfree will probably not increase but R will drop)? - analogous to the disordered side-chain atoms, bulk solvent atoms are of course also present in the crystal, so why not fill the AU with solvent molecules and let refinement take care of them? (published methodology, see https://doi.org/10.1107/S0907444906021627 <https://doi.org/10.1107/S0907444906021627>) Trimming or non-evidence-based placement and refinement are somehow halfhearted options with split opinions among the community as the discussions demonstrate. Adding/Modelling a plausible side-chain rotamer with zero occupancy still has its charm and better reflects the situation "the side-chain atoms must be there but we do not know exactly where"…….. Cheers Jeroen ######################################################################## 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/
