Dear all, Coming back to map blurring...
> On 24 Nov 2020, at 16:41, John R Helliwell <jrhelliw...@gmail.com > <mailto:jrhelliw...@gmail.com>> wrote: > > [...] Coot’s blurring and sharpening tool is tethered directly to one’s > measured diffraction data. > [...] But, I have just rechecked the Coot manual and see no reference. The use of Coot's blurring tool is briefly recommended in the context of ligand binding analysis on page 12 of this publication: https://doi.org/10.1107/S2059798316020143 <https://doi.org/10.1107/S2059798316020143>. This is so useful in cryo-EM that the technique of simultaneously viewing multiple maps with different levels of blurring/sharpening as a visual confirmatory aid has become routine (https://doi.org/10.1107/S2059798318007313 <https://doi.org/10.1107/S2059798318007313>). More generally, map blurring can be useful for exploring evidence for the presence of structure in the crystal that is currently missing from the model in both MX and cryo-EM. Regards, Rob > On 27 Nov 2020, at 08:41, Clemens Vonrhein <vonrh...@globalphasing.com> wrote: > > Dear Nika, > > as a possible alternative or second opinion, you could have a look at > the ligand-detection modes [1] in BUSTER too - see e.g. > > https://www.globalphasing.com/buster/wiki/index.cgi?LigandDetectionModes > > It's very similar to the Phenix Polder maps - so might not tell you > anything different, but looking at results from different > implementations can be useful as a check. > > Anyway, one of the main problems handling partially occupied ligands > (and let's ignore the possibility of partial disorder for > "simplicity") is that you might have a mixture of three models within > your binding site: (1) compound, (2) waters (at ordered positions when > the ligand is not bound) and (3) bulk solvent (at disordered positions > when the ligand is not bound). > > What can be useful is to include at least the alternative ordered > water model (from a well refined APO model?) and then refine the > (grouped) occupancies: > > OCC(compound) + OCC(waters) = 1.0 > > This way you give the refinement the option to chose between two > alternative interpretations [2]. To avoid any bias in that refinement > procedure, you could start from two extremes: once with > OCC(compound)=0.9 and once with 0.1. If the OCC(compound) refines to a > small value (say <0.2 or such) in both cases, it is possibly not really > there. > > Cheers > > Clemens > > [1] Vonrhein, C. and Bricogne, G., 2005. Automated structure > refinement for high‐throughput ligand detection with > BUSTER‐TNT. Acta Crystallogr. Sect. A, 61, p.c248. > [2] > http://www.globalphasing.com/pipermail/buster-discuss/2015-August/000255.html > > On Tue, Nov 24, 2020 at 11:28:42AM +0000, Nika Žibrat wrote: >> Hello, >> >> >> I have a question about protein-ligand, of which ligand displays an >> ambiguous electron density. I am solving a structure of protein with ligand >> which was obtained via soaking. Structural characteristics indicate the >> ligand is present however the electron density is quite vague and too small >> for the size of the whole ligand. I did a Polder map which showed much >> larger area of green density. After insertion of my ligand into the green >> density in Polder I ran phenix.refine and there is a lot of red on the spot >> where the ligand is which was to be expected. This leaves me wondering how, >> if even do I incorporate the polder map data into my refine input. >> >> >> My question is, how do I continue refining and validating the structure in >> this case? >> >> >> Thank you, >> >> >> Nika Žibrat >> >> >> ######################################################################## >> >> 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/ > > -- > > *-------------------------------------------------------------- > * 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/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/
