Re: [Jmol-users] Version 12.08

[Robert H. <ha...@st...>]

On Mon, Aug 23, 2010 at 8:41 AM, Pshemak Maslak <pm...@ch...> 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
>
>
>
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-- 
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