Hi Fellows, I'd really like to emphasize the point in the Buster instructions "be careful when examining fo-fc at low levels" when solvent is excluded. If the solvent contribution is omitted where you suspect the ligand (e.g. occupancy 0.02 in Refmac), there will be a fo contribution there from the solvent that is there. Particularly if that solvent is a dense solution, that fo component will show up nicely and at not so low difference map levels, and in the shape of that 'excluded' ligand.
Figure 2 in link illustrates that. https://febs.onlinelibrary.wiley.com/doi/epdf/10.1111/febs.14320 If you start to fill that void with multiple ligands of various low occupancies, you are effectively modelling disordered solvent. This is particularly tempting because I found multiple cases where the classical RSR and RSCC measures give acceptable stats for such models. The hunt for low occupancy ligands then quickly becomes murky density fishing business... Best, BR -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Clemens Vonrhein Sent: Friday, February 8, 2019 09:53 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Turning off the bulk solvent modelling in Refmac5 to generate Polder maps? Dear Samuel, On Mon, Feb 04, 2019 at 11:39:58AM +0000, Samuel Davis (PG Research) wrote: > I'm wondering if anyone knows if it is possible to turn off the bulk > solvent modelling in Refmac5, for the purpose of generating Polder > maps? I know that an option for Polder maps is directly implemented in > Phenix, but we ideally want to use Refmac5, as we have used it for the > rest of our refinement and want to keep it consistent if possible. And if you want to try the original implementation of the underlying idea as an alternative, have a look at the ligand detection mode and maps [1] produced by BUSTER [2]. See also [3] and some early examples of their usefulness [4-5]. Cheers Clemens [1] https://www.globalphasing.com/buster/wiki/index.cgi?LigandDetectionModes [2] https://www.globalphasing.com/buster/ [3] Vonrhein, C., & Bricogne, G. (2005). "Automated Structure Refinement for High-throughput Ligand Detection with BUSTER-TNT". Acta Crysta A61, C248. [4] Thoma, Ralf, et al. "Insight into steroid scaffold formation from the structure of human oxidosqualene cyclase." Nature 432.7013 (2004): 118. [5] Ekroos, Marika, and Tove Sjogren. "Structural basis for ligand promiscuity in cytochrome P450 3A4." Proceedings of the National Academy of Sciences 103.37 (2006): 13682-13687. -- *-------------------------------------------------------------- * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * Global Phasing Ltd., Sheraton House, Castle Park * Cambridge CB3 0AX, UK www.globalphasing.com *-------------------------------------------------------------- ######################################################################## 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
