OK, I misinterpreted the scaling differences in my previous report. The problem appears to be a simple scaling factor difference between Jmol's isomesh cutoff value and PyMOL's isomesh sigma value. (Contrary to my previous interpretation, I don't think the scaling varies from the center of the molecule.)
However, I now notice that the scale factor (cutoff vs. sigma ratio that makes the two isomeshes the same) varies with the size of the molecule loaded. Detailed demonstrations are at the top link on this list: http://www.umass.edu/molvis/tests/ -Eric --- On Fri, 2/19/10, Robert Hanson <[email protected]> wrote: > From: Robert Hanson <[email protected]> > Subject: Re: [Jmol-users] Problem w/ electron dens. maps > To: [email protected] > Date: Friday, February 19, 2010, 7:40 PM > Exactly the problem. We have wildly > different data sets -- from electron diffraction to X-ray > data. Where did we end up with that discussion about sigma? > I can certainly look at the Pymol code and see what Warren > did there. > > > Bob > > On Fri, Feb 19, 2010 at 11:37 AM, > Thomas Stout <[email protected]> > wrote: > > > But electron density maps can be on arbitrary scales, so > the value "1.0" may very well be meaningless > (except in the particular case where normalization has made > 1.0=1e-/A**3), and will certainly produce wildly different > results from dataset to dataset depending on the provenance > of each particular dataset (scale factors, etc). The > "standard" in macromolecular crystallography is to > view density maps at 1.0sigma & "difference > maps" at 3.0sigma. > > > > -Tom > > > On > Fri, Feb 19, 2010 at 7:49 AM, Robert Hanson <[email protected]> > wrote: > > > Eric, I think this is just that Pymol has a different > definition -- 1.0 sigma is not 1.0 value. Jmol uses actual > value 1.0, not "sigma" 1.0. > > Bob > > > On Fri, Feb 19, 2010 at 7:26 AM, Eric Martz <[email protected]> > wrote: > > Dear Bob, > > > > I'm sorry to report that Jmol 11.9.29 is not displaying > ccp4 electron density maps correctly as isomeshes. I have > demonstrated a major problem here (hopefully not major to > fix): > > > > http://www.umass.edu/molvis/tests/jmol_edm_test5/ > > > > -Eric > ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
