Thanks Bob. I understand that that there are some builtin settings for
the application that you want to rely on for a consistent look&feel so
that is the way it is currently set.
One of my points is that the available preference settings within the app
do not let a user (or a distributor) configure it for non-expert users.
I agree that the program should not change the information read from the
CIF, it is best to assume that what is in the file is exactly what the
creator of the file intends to be there.
But that, in a way, is the point, the default should be to display what is
in the CIF only. What the app is doing is displaying the atoms but in the
context of the unit cell with a non-intuitive rotation center. I'd argue
strongly that the default should display the atoms at the coordinates
given in the CIF with the rotation center at the center of mass of those
atoms.
Do you have any thoughts on how to make the app more user configurable?
How are the preferences and configuration parameters stored now? If I want
to provide the Jmol.jar file for my chemists to download to their
(windows,linux,mac) machines what do I need to do to preset the app to
have fuller menus and a particular set of preferences?
Rich
On Thu, May 1, 2008 4:41 pm, Bob Hanson wrote:
> Rich, thanks for the feedback. Users can set their own defaults in Jmol
> for the application, but I hear you about first-time or casual users.
>
> This was discussed some time ago, and we ended up with these defaults,
> so I guess I'm saying those are what we are going to use. (Not to be
> dismissive.) The issue is that different CIF formats file the data
> different ways. The default is to show the file data as is -- without
> manipulation. That's consistent with all other file load formats.
>
> Now, if you want something else, you can specify either
>
> load "filename" {555 555 1}
>
> or
>
> load "filename" {555 555 0}
>
> to change the default loading. If you have a data set that cuts
> molecules into pieces, then one of these formats along with
>
> display molecule=1
>
> should pull up the full molecule.
>
> [EMAIL PROTECTED] wrote:
>
>>I've had a look at both 11.4.2 and 11.5.33 and I don't think the default
>>setup of the application is appropriate for new/casual users of chemical
>>crystallography information.
>>
>>When fed a CIF the application puts up a unit cell box with one molecule
>>with the center of rotation not coincident with the center of mass of the
>>displayed molecule.
>>
> This is simply what was in the CIF file. Directly. No changes.
>
>>This is unexpected. Looking through the menu items
>>doesn't show any way of setting this to a more conventional view. A lot
>> of
>>the choices for control of the display don't appear until the
>> right-button
>>pop-up menu is discovered.
>>
>>
> The application doesn't have a robust menu system. That's agreed. We
> need help on that.
>
>>>From a usability perspective most of what is in the right-button menu
>>should be in the application menus (and sub menus). The pop-up menu
>> should
>>be limited to those things that are relevant to being affected for the
>>item under the pointer at the time the right-button is clicked.
>>
>>
>>
> The Jmol application could definitely use some work in this regard.
>
> Bob
>
>>Rich
>>
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>
>
> --
> Robert M. Hanson
> 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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