Peter & Gabrielle, Though I can't say for certain what Gabrielle is seeing, generally speaking there is some ambiguity with visualization tools as to how map data is to treated: Some map file formats are normalized by convention (in the file data itself) and others do not. Some visualization tools automatically normalize maps upon reading, others do not.
PyMOL's default behavior is dependent upon map file type: CCP4 and O/BRIX/DSN6 maps are automatically normalized upon reading (disable via "normalize_*" settings), other maps types are not. PyMOL's normalization is a straight statistical average of all map points -- this may or may not be what you want. If migrating to PyMOL from another tool, then it is definitely worth comparing how the maps are being represented by creating an equivalent figure in both, making sure that they match, and if they do not, then figuring out why not. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info "Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor!" -WLD > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of Peter Adrian Meyer > Sent: Friday, March 02, 2007 9:40 AM > To: Gabrielle Malo > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] contour levels in pymol > > > > a mystery to me. Why is there a difference bewteen contour > levels of > > FFT electron density maps displayed in Xfit vs pymol? When > using the > > command for example :isomesh mesh1, fo-fc, 1.0, etc..., in > pymol what > > does 1.0 in terms of sigma level really mean. I was under the > > assumption that 1.0 sigma is equal to 1.0 sigma as defined > by FFT, but > > then there would not be a difference in the two maps > displayed at this > > value in the two programs, which there is. Can anyone help clarify > > this issue? > > I was confused about this myself a few months back. The > sigma level comes from the rms deviation of the map, not the > fft itself. So if the maps are different (different sizes, > covering different regions, or calculated using different > grid spacints), then the sigma levels won't necessariily be > equivalent. > > If all of the map parameters are the same and you still get > differences in the displayed maps for the two programs, then > there's something else going on. > > Pete > > > Pete Meyer > Fu Lab > BMCB grad student > Cornell University > > > -------------------------------------------------------------- > ----------- > Take Surveys. Earn Cash. Influence the Future of IT Join > SourceForge.net's Techsay panel and you'll get the chance to > share your opinions on IT & business topics through brief > surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge > &CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
