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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