The thing to do is to set up a script file that does that:
q = getProperty("orientationInfo.quaternion");
select *;
rotateSelected @q;
reset
When you save the file, it will have the changed coordinates.
On Thu, May 2, 2013 at 11:09 AM, James Ryley <[email protected]> wrote:
> Greetings,****
>
> ** **
>
> I’ve been using JMol for a while, mostly via scripting. It has been very
> useful for me, and Robert Hanson has been kind enough to answer some
> questions for me concerning particular ways of outputting graphics. So
> thanks to everyone working on this! Note that I did search the list archive
> for this topic, and while I see related posts, nothing on this exactly.***
> *
>
> ** **
>
> I’m wondering why there isn’t a simple “save” or “save as” that outputs a
> .hin (or .pdb) file instead of a proprietary file like “save STATE” or
> “save ORIENTATION” generates. To be sure I am understanding this correctly,
> what I believe happens is this:****
>
> ** **
>
> **1) **Open a molecular model (I’ve using mostly .hin)****
>
> **2) **Rotates the model, or set rendering options.****
>
> **3) **“save STATE” or “save ORIENTATION”****
>
> **4) **JMol doesn’t alter the original input file. It generates an
> additional STATE or ORIENTATION file that essentially says “If you take the
> input file and rotate it like this (and then maybe also set options x, y,
> and z) you’ll get back what you want.”****
>
> ** **
>
> The additional STATE or ORIENTATION file calls the original file, so you
> cannot rename the base file or move it without editing the additional file,
> and far more importantly, you cannot use other programs to read the updated
> model, because while they can read the base .hin file just fine, they will
> not know how to deal with the parameters in the extra files.****
>
> ** **
>
> There is one way around this that I know of, and it cannot be done in the
> GUI, because it doesn’t work with mouse-based rotation, nor does it even
> work with script-based “rotate” unless you “select ALL” first and then use
> “rotate selected.” Specifically, via the scripting interface:****
>
> ** **
>
> **1) **select ALL****
>
> **2) **rotate selected x 45 y 60 z 90****
>
> **3) **write c:\test.pdb****
>
> ** **
>
> The .pdb file is written in the new orientation.****
>
> ** **
>
> Since I just described a work-around, what’s the problem? Just that it’s
> really clunky when you want to adjust a model visually, as opposed to via
> scripting, and save it in the new orientation. For example, I open a model,
> spin it around to get just the right view I want to show someone else or to
> export a graphic, and I can’t just hit “save”. Rather, I would need to do
> something like this:****
>
> ** **
>
> **1) **Rotate with the mouse****
>
> **2) **Use script to:****
>
> **a. **getProperty orientationInfo.rotateXYZ****
>
> **b. **select ALL****
>
> **c. **rotate selected x 45 y 60 z 90 (and somehow those numbers got
> parsed out of the getProperty response – not sure how to do that off the
> top of my head, and maybe there needs to be an orientation reset in here
> also so that you aren’t rotating farther from the already-correct position)
> ****
>
> **d. **write c:\test.pdb****
>
> ** **
>
> Obviously, that’s not terribly arduous, but a “save” button would be a lot
> easier, especially when dealing with many models. Am I missing something
> obvious, or is there actually no simple GUI-based way to do this?****
>
> ** **
>
> Sincerely,
> James R****
>
> ** **
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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