[Jmol-users] Is there a problem with isosurfaces in jmol-14.6.4_2016.10.02?

2016-10-28 Thread fziegler 
I have been using jmol-14.2.9_2014.11.23 to make electrostatic potential maps. 
[See: http://ursula.chem.yale.edu/~chem220/chem220js/StudyAids.html#ESP] 


I use Gaussian to generate cube files. I open jmol.jar>console and type:

$ isosurface cutoff 0.02 filename_den.cub map filename_esp.cub
$ write isosurface filename.jvxl

All is well.

I downloaded jmol-14.6.4_2016.10.02

The console does not appear to work properly. If the line $ isosurface cutoff 
0.02 filename_den.cub map filename_esp.cub is added, blue text appears with 
cutoff 0.0.

Typing $ write isosurface filename.jvxl gives only a return of the prompt $. No 
jvxl file is written. Multiple entries do not work. Jmol.jar must be closed and 
reopened to make an entry. Still no positive result.

I have taken jmol.jar from jmol-14.2.9_2014.11.23 and put it in 
jmol-14.6.4_2016.10.02. It works but places the file in the former Jmol folder. 
I can redirect the jvxl file with write isosurface /Users/…/filename.jvxl.

But this not an advantage. 

Is there a problem with jmol.jar in mol-14.6.4_2016.10.02?

Thanks for your help, Fred Ziegler--
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[Jmol-users] I there a problem with isosurfaces in jmol-14.6.4_2016.10.02

2016-10-28 Thread fziegler 
I have been using jmol-14.2.9_2014.11.23 to make electrostatic potential maps. 
[See: http://ursula.chem.yale.edu/~chem220/chem220js/StudyAids.html#ESP]

I use Gaussian to generate cube files. I open jmol.jar>console and type:

$ isosurface cutoff 0.02 filename_den.cub map filename_esp.cub
$ write isosurface filename.jvxl

All is well.

I downloaded jmol-14.6.4_2016.10.02

The console does not appear to work properly. If the line $ isosurface cutoff 
0.02 filename_den.cub map filename_esp.cub is added, blue text appears with 
cutoff 0.0.

Typing $ write isosurface filename.jvxl gives only a return of the prompt $. No 
jvxl file is written. Multiple entries do not work. Jmol.jar must be closed and 
reopened to make an entry. Still no positive result.

I have taken jmol.jar from jmol-14.2.9_2014.11.23 and put it in 
jmol-14.6.4_2016.10.02. It works but places the file in the former Jmol folder. 
I can redirect the jvxl file with write isosurface /Users/…/filename.jvxl.

But this not an advantage. 

Is there a problem with jmol.jar in mol-14.6.4_2016.10.02?

Thanks for your help, Fred Ziegler
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Re: [Jmol-users] rotate best? DOCUMENTATION

2016-10-28 Thread Robert Hanson 
done
​
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Re: [Jmol-users] rotate best? DOCUMENTATION

2016-10-28 Thread Eric Martz 
Right! I did not have all atoms selected. I suggest a change "best 
orientation for viewing" to "best orientation for viewing the selected 
atoms". And change "the model's containing box" to "the containing box 
of the selected atoms". It never occurred to me to select all first. 
Also I had difficulty understanding "thinnest along the line of site". 
(It should be "line of sight"). I suggest "thinnest front to back".


Jean-Baptiste: do "select all" before you "rotate best".

Bob: Thanks!

-Eric

On 10/28/16 12:59 PM, Robert Hanson wrote:



On Fri, Oct 28, 2016 at 11:09 AM, Eric Martz 
> wrote:


1. When I apply "rotate best" to 1d66, I expect the distance from the
frontmost to backmost atoms to be minimized, and the distance from the
leftmost to rightmost atoms to be maximized. Neither appears to
happen.
Do I misunderstand the goal?


works for me. What are you seeing? Do you have all the atoms selected?

" Rotates the model to a calculated "best" orientation for
viewing, such
that the model's containing box is thinnest along the line of site
(z),
and widest horizontally (x)."


That should read -- such that the box containing /the selected atoms/

When I apply "rotate best" to 3hyd (a linear peptide), the top to
bottom
distance seems to be minimized and the left to right maximized,
with the
front to back intermediate.

If "rotate best" is working properly, could someone please explain
it to me?

2. Are there any other commands that automatically rotate the model to
an optimal orientation? It appears to me that "moveto
front|top|bottom|left|right|back" relates to the initial (reset)
orientation, not to any "optimal" orientation.


Just that  one.

Thanks, Eric



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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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



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Re: [Jmol-users] rotate best?

2016-10-28 Thread Robert Hanson 
On Fri, Oct 28, 2016 at 11:09 AM, Eric Martz 
wrote:

> 1. When I apply "rotate best" to 1d66, I expect the distance from the
> frontmost to backmost atoms to be minimized, and the distance from the
> leftmost to rightmost atoms to be maximized. Neither appears to happen.
> Do I misunderstand the goal?
>
>
works for me. What are you seeing? Do you have all the atoms selected?


> " Rotates the model to a calculated "best" orientation for viewing, such
> that the model's containing box is thinnest along the line of site (z),
> and widest horizontally (x)."
>
>
That should read -- such that the box containing *the selected atoms*



> When I apply "rotate best" to 3hyd (a linear peptide), the top to bottom
> distance seems to be minimized and the left to right maximized, with the
> front to back intermediate.
>
> If "rotate best" is working properly, could someone please explain it to
> me?
>
> 2. Are there any other commands that automatically rotate the model to
> an optimal orientation? It appears to me that "moveto
> front|top|bottom|left|right|back" relates to the initial (reset)
> orientation, not to any "optimal" orientation.
>
>
Just that  one.


> Thanks, Eric
>
>
> 
> --
> The Command Line: Reinvented for Modern Developers
> Did the resurgence of CLI tooling catch you by surprise?
> Reconnect with the command line and become more productive.
> Learn the new .NET and ASP.NET CLI. Get your free copy!
> http://sdm.link/telerik
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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
--
The Command Line: Reinvented for Modern Developers
Did the resurgence of CLI tooling catch you by surprise?
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[Jmol-users] rotate best?

2016-10-28 Thread Eric Martz 
1. When I apply "rotate best" to 1d66, I expect the distance from the 
frontmost to backmost atoms to be minimized, and the distance from the 
leftmost to rightmost atoms to be maximized. Neither appears to happen. 
Do I misunderstand the goal?

" Rotates the model to a calculated "best" orientation for viewing, such 
that the model's containing box is thinnest along the line of site (z), 
and widest horizontally (x)."

When I apply "rotate best" to 3hyd (a linear peptide), the top to bottom 
distance seems to be minimized and the left to right maximized, with the 
front to back intermediate.

If "rotate best" is working properly, could someone please explain it to me?

2. Are there any other commands that automatically rotate the model to 
an optimal orientation? It appears to me that "moveto 
front|top|bottom|left|right|back" relates to the initial (reset) 
orientation, not to any "optimal" orientation.

Thanks, Eric


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