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/
