If, as Paul says, the "smooth" map is just more finely sampled than a not smooth one, there is no doubt. The smooth map is a more accurate representation of the electron density map, which is in fact a continuous function.
The sampling of a map on a grid is a computational simplification of the map. This approximation is made for the convenience of the computer software. I presume that Coot's real space refinement includes corrections for the course size of the grid, but such corrections usually assume that the variation of the map function between grid points is linear. The finer the grid the more accurate these corrections will be. Paul knows the properties of his software so he is the best source for the effect of grid size on the real space refinement software and his default sampling rate will be good enough, but a finer grid can't hurt other than slowing the calculation. Dale Tronrud On 11/20/2019 11:36 AM, Daniel Larsson wrote: > Hi Karim, > > If in doubt, you can load both maps and use the original one for > refinement but hiding it and use the smooth map for visualization. > > Regards, > Daniel > > >> On 20 Nov 2019, at 14:28, Karim Rafie <[email protected] >> <mailto:[email protected]>> wrote: >> >> Dear all, >> >> I have a question regarding the map smoothening option in coot >> (Calculate -> Map Tools -> Make a (very) smooth copy). If I understand >> correctly, the Shannon sampling factor applied by default is 1.5 and >> that the smoothening process adjusts that factor. >> Does that have any effect on the validity of the map, i.e. can I still >> use it for model builduing or will it "smoothen-out" possibly >> important data? >> >> Any help would be greatly appreciated. >> >> Best wishes, >> Karim >> ############################################## >> Karim Rafie; PhD, AMRSC >> Postdoctoral Research Fellow >> Carlson Lab >> Department of Medical Biochemistry and Biophysics >> Umeå University >> Umeå / Sweden >> >> ------------------------------------------------------------------------ >> To unsubscribe from the COOT list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 > > Page Title > > > > > > > > När du har kontakt med oss på Uppsala universitet med e-post så innebär > det att vi behandlar dina personuppgifter. För att läsa mer om hur vi > gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ > > E-mailing Uppsala University means that we will process your personal > data. For more information on how this is performed, please read here: > http://www.uu.se/en/about-uu/data-protection-policy > ------------------------------------------------------------------------ > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
