Hi, this is why Polder map tool also includes analysis of the map in question to determine whether it looks like bulk-solvent or something else, as described in paragraph 5 here: http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf This analysis tells you in plain English what you are likely to look at. Otherwise I agree that making sense of maps in solvent-excluded regions are very tricky. Pavel
On Fri, Feb 8, 2019 at 2:32 AM Bernhard Rupp <hofkristall...@gmail.com> wrote: > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
