Hi Nika, - As Herman wrote, you should use common sense to interpret a polder map: if the ligand is not there, this kind of map may show only bulk solvent. So the appearance of some density in the area of the ligand does not "prove" that the ligand is there. Also, map interpretation should be done while keeping in mind data quality, data resolution and the state of the model (how far along you are in refinement). Ligand density may not be clear yet if the model is fresh out of MR, but it may become better once the model is finalized. At high resolution, negative density may appear if the occupancy is too high and it may disappear if you refine it (of course, don't let it refine to unreasonably low occupancy...).
- There is no need to refine against a polder map. If the ligand is placed in the model, the bulk solvent mask is calculated accordingly, so refinement is aware that there is no bulk solvent in this area. I wrote the polder tool, so if you want, I can have a look at the maps. Send me the model with the refined ligand + data (+ cif restraints if applicable). If you send files, be mindful to do so off-list (reply only to me). Best wishes, Dorothee On Tue, Nov 24, 2020 at 3:29 AM Nika Žibrat <[email protected]> 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 > -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org ######################################################################## 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/
