Well, this web site http://macxray.chem.upenn.edu/gam/9129b.html is
still using 11.0.2, so that won't help. You need to download 11.1.39.
I think what the problem is is that you are trying to use "symop=3555"
and it is not what you think it is. Your page suggests that what you
want to do is show the base atoms and then a set of symmetry-related
atoms, possibly shifted. That sound about right?
Then what you need to do is
a) load "" {555 555 0}
This loads the base atoms and the symmetry operation-related atoms. No
normalization is done, so many of these atoms will be outside cell 555.
b) do something like this:
function getOperation() {
var sym = "1";
for (i = 0; i < document.myForm.myRadio.length; i++) {
if (document.myForm.myRadio[i].checked) {
sym = document.myForm.myRadio[i].value;
}
}
var a = document.myForm.mySelect1.value // -1, 0, or 1 -- not 4, 5, or 6
var b = document.myForm.mySelect2.value // -1, 0, or 1 -- not 4, 5, or 6
var c = document.myForm.mySelect3.value // -1, 0, or 1 -- not 4, 5, or 6
var cmd = 'save orientation;load "" {555 555 0};selectionHalos
on;select symop='+sym+';translateselected {'+a+'/1 '+b+'/1
'+c+'/1};display not symmetry or selected;restore orientation'
return cmd
}
and
<input onclick='jmolScript(getOperation())' value="Add/Move"
type="button">
So what we are doing is loading one unit cell, without normalization.
then we are selecting a symmetry operation, moving those atoms as
desired, and displaying just the original atoms and the selected ones.
The save/restore orientation hides the reload.
I'm pretty sure that's what you are really after.
The other thing that I think is confusing you here is that the symmetry
operations you define are not expressed the way they are in the file.
You have:
x, y, z
x,½ - y, ½ + z
-x, -y, -z
-x, ½ + y, ½ - z
but from
show symmetry
we get:
Spacegroup: P 21/c
Number of symmetry operations: 4
Symmetry Operations:
x,y,z
-x, y+1/2, -z+1/2
-x, -y, -z
x, -y-1/2, z-1/2
Now, I know, these are the same, but if you really want to talk about
them and translate them and such, I think you should show the correct ones.
I would recommend just getting the operator straight from the file.
Something like this (which requires the latest Jmol.js):
var isdone = false
function getRadios() {
if (isdone)return;
isdone = true;
var Operations = jmolEvaluate('script("show
symmetry")').split("Symmetry Operations:")[1].split("\n")
var s = ""
for (var i = 0;i < Operations.length - 1;i++)
if (Operations[i].length > 0)
s+='<input name="myRadio" value="'+ i +'"
type="radio">'+Operations[i]+ '<br>'
document.getElementById("radios").innerHTML = s
}
with:
<div id=radios>
<a href=javascript:getRadios()>Get Symmetry Operations</a>
</div>
and, just to top it off, and a loadStructCallback to put those radio
buttons in automatically:
jmolApplet(500, "zap; set loadstructcallback = \"getRadios\";
set echo middle center; font echo 18 sanserif bold; color echo yellow;" +
"echo Loading cell|It could take a while||Please wait...; delay
0.5; load 9129b_files/9129.cif {444 666 0};" +
"zoom 150; restrict symop=1555;" +
"cpk 15%; wireframe 0.10; unitcell 0.05; color unitcell
lightblue; color boron SkyBlue;" +
"color carbon LightGrey; set perspectiveDepth OFF;
selectionHalos on; set measurements ANGSTROMS;" +
"select none; center{1/2,1/2,1/2}; set axesUnitCell; set axes
0.05; color axes red;" +
"set displayCellParameters OFF");
Bob
P.J. Carroll wrote:
>Bob,
> I'm also getting some similar weird behavior - if I
>explicitly select 3555 it appears where 3666 should be AND 3444
>appears where 3555 should be.
>
>
That's the shifting business I just fixed.
> BUT now I can't seem to get the same behavior with the
>buttons on my webpage! I'm confused??
>
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