Hello- I need some advice on MEP display script. When I use the following script:
isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6 MOLECULAR color map mep;isosurface translucent;delay 2; echo; I get proper MEP's for most molecules, but some molecules present problems. For example, m-nitrophenol's MEP is completely blue (colors = "roygb") even though the partial charges in the file are reasonable. If I use the following script, which inserts "range all," then the above problem disappears, but the simple sequence ethane, ethene, ethyne is a bit disappointing - colorful, but disappointing: isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6 MOLECULAR color range all map mep;isosurface translucent;delay 2; echo; The "point" is still captured in these latter hydrocarbon displays, but this raises two questions: 1) I thought "range all" was default, but there must be another default. What is the default range in the above script context? 2) I think my first line of script above comes close to the Jmol left click menu script of "isosurface delete resolution 0 molecular map MEP translucent." Indeed, the menu produces the same blue m-nitrophenol (o and p as well). What is the current recommendation for a MEP script? Again, the partial charges in the files are reasonable, and they can be read by a direct call to: select; wireframe 0.03; spacefill 1%; spacefill 1%;label \"%-8.3[partialcharge]\"; Otis -- Otis Rothenberger http://chemagic.org ------------------------------------------------------------------------------ Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
