Bob- While playing around with color range values, I found the source of one problem, but I still have a couple of questions.
The nitrophenols problem is bad data. I used Accelrys Discovery Visualizer to draw and calculate these files. For the conanical structure that I drew, there should have been a formal charge on the nitrogen and on one of the nitro oxygens. The file only had the N formal charge. Consequently, the partial charges did not equal zero. This playing brings up a new question. I also still have a problem with my original question. 1. New question: We use Accelrys and Spartan to generate data. Accerrys calculates partial charge in nC and Spartan calculates this charge as esu. I never noticed this before. I assume that as long as partial charge sums to zero, Jmol will produce that same MEP, providing off course that the data is good and the calculations are comparable. Is this a correct assumption? 2. While the Jmol right click menu MEP code is now looking much better to me, I don't understand why the following two JavaScript snips produce drastically different results. This JS is fed to my evalRasmol() function. The data in the second example is ethane from Accelrys: A) isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6 MOLECULAR color range all map mep;isosurface translucent;delay 2;echo; B) isosurface COLORSCHEME '" + colors + "'; isosurface resolution 6 MOLECULAR color range -0.068 +0.023 map mep;isosurface translucent;delay 2;echo; If -0.068 and +0.023 are the Accelrys min and max, shouldn't the two code snips produce similar MEPs? As a point of information both Accelrys data and Spartan data for ethane produce: A) ROYGB all light up and ethane does, indeed, look like a nucleophile. Actually, this is what I expected "all" to do. B) More like the Jmol default. I expected that this would be the same as A - i.e. min to max = "all" Again, a point of information: Snip B) with -0.05 +0.05 essentially produces the Jmol menu MEP for both Spartan data and Accelrys data. 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
