From: Robert H. <ha...@st...> - 2010-09-18 23:13:11
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It depends upon which type of surface is generated -- sasurface and solvent specifically do ignore water. The others (vdw, moleular) do not. I'll note that. Just use "solvent" instead of "molecular" -- no need to change files! Not planning to change any defaults. On Sat, Sep 18, 2010 at 11:27 AM, Eric Martz <em...@mi...>wrote:It de > > 2. I want to color the surface by MEP. It appeared that I had no problems > setting the partial charges with > > {hydrogen}.partialCharge = 0.41 > #{oxygen}.partialCharge = -0.82 > {nitrogen}.partialCharge = -0.82 > > The documentation says that > > isosurface resolution 6 solvent map mep > > will use the partialCharge atom properties. It did not (surface was all > blue). Is this a bug or a problem in the documentation? > > should work -- works for me... Check the data range, which is reported when you do the default mapping. The default for MEP is just -0.1 to 0.1. Your values are probably all > 1. isosurface vdw map color range -1 1 mep for examples. > 3. The MEP section of the isosurface documentation says that "if MEP is > followed by PROPERTY xxxx" it will be used instead of partial charges. > However, > > isosurface resolution 6 solvent map MEP property partialcharge > > produced an all-blue surface. Is this a bug? > > just that range problem -- you haven't set a decent range. > 4. In order to color the surface, I omitted "MEP": > > isosurface resolution 6 solvent map property partialcharge > > This produced the default yellow-green-blue surface. But I want a > red-white-blue surface as is conventional for MEP. OK, so this worked > > right - but it's not a MEP. Just charges. you need also before MEP or PROPERTY: colorscheme "rwb" or colorscheme "bwr" or after the isosurface command, you need color isosurface "bwr" or color isosurface "bwr" range 5.0 10.0 or such. > isosurface resolution 6 solvent map MEP property partialcharge colorscheme > "rwb" > > except that the "red" was pink and the "blue" was deep blue, despite the > isosurface report claiming "isosurface full data range -0.82 to 0.41 with > color scheme spanning -0.82 to 0.41". > > must have been a trace of red in there somewhere. > I tried a few things to get a redder color at the reddest end of the > colorscheme, without success. > > Is there some way I can get the "red" in the "rwb" color scheme to be > redder (more saturated)? > > just change your color scheme range to something like -0.5 to 0.41 Bob > Thanks! -Eric > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 |