On Mon, Aug 23, 2010 at 8:41 AM, Pshemak Maslak <[email protected]> wrote:
> Hello,
>
> First of all Jmol is an amazing program and I am extremely impressed by
> its rapid growth since I started using it about two moth ago. I have
> difficult time keeping up with the updates. Kudos to the developers!
>
>
> I have just replaced version 11.8 with 12.08. Since I am still very new
> to Jmol some of the questions or comments are most likely due to my
> ignorance, but here they go:
>
good move -- we do want to know ANYTHING that behaves differently between
these for you.
>
> 1. It looks like in contour plots (or equivalent color-filled
> projections) hovering above contour line or a color border does not
> display the values associated with that line. It did in 11.8 version.
>
set drawHover true
The problem was that one doesn't necessarily want that sort of
functionality, and there was no way to turn it off.
>
> 2. The isosurface (mostly orbitals) calculations seem slower with 12.08
> than with 11.8. I did not do any quantitative comparison, but that is my
> impression upon checking on several different computers.
>
I thought I noticed that with molecular surfaces as well, but I haven't been
able to track it down.... I am seeing some oddities in timing for isosurface
creation, but nothing so dramatic.
>
> 3. Display results differ (slightly) between versions. For example:
>
>
> isosurface estrans2 cutoff 0.09 phase color darkred darkblue color
> translucent atomicOrbital 2 0 0 1.0; isosurface escross2s color absolute
> -0.2 0.40 plane xy resolution 6 atomicOrbital 2 0 0 1.0
>
>
> gives somewhat different relative sizes of the contour (colored
> cross-section) and orbital boundary. BTW: Is there a way to plot
> contour or color-filled-projections of electron density rather than the
> wavefunction?
>
You mean the square of psi, right? Yes, it's the SQUARED parameter, but I
think there is a bug there...
> 4. 12.08 has difficulty in displaying jvxl file written by 11.8. It does
> it very slowly (several minutes) and --after finally loading -- the
> model cannot be interacted with. I have encountered only one example of
> this difficulty, and the jvxl file re-written with 12.08 Jmol works
> fine. Could this have anything to do with the changes in the spartan
> file reader? (my jvxl files are based on smol spartan files)
>
send me one of these JVXL files so I can see it, along with the model file.
Best is if you
write toBob.jmol
and just send me that file.
>
> I had to add noOrient filter for several of my other structres to
> recover the previous model orientation. BTW: a suggestion: perhaps the
> listings of new features in the new versions (such as this one:
> http://chemapps.stolaf.edu/jmol/docs/examples-12/new12.htm) should
> separately highlight changes that result in different behavior in the
> new version. It would help (at lest novices like me) to make adjustment
> when changing to a new version.
>
Quite possibly. That is one of the very few changes -- I will note it in the
documentation. Spartan files now open to the exact orientation left by the
Spartan user. This allows for smooth transition from Spartan to Jmol.
>
> Thank you again for your work on Jmol and your help in learning how ti
> use it.
>
> PM
>
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by
>
> Make an app they can't live without
> Enter the BlackBerry Developer Challenge
> http://p.sf.net/sfu/RIM-dev2dev
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> 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
------------------------------------------------------------------------------
Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
Be part of this innovative community and reach millions of netbook users
worldwide. Take advantage of special opportunities to increase revenue and
speed time-to-market. Join now, and jumpstart your future.
http://p.sf.net/sfu/intel-atom-d2d
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
