Steve,
Besides the fact that you found some apparently incorrect data in one
of the CIF files, your initial question relating to the oxygens and
other atoms oddly displaced has to do with the way Jmol applies the
symmetry operators. In some cases, as you see there, just loading a
single unit cell
I'll definitely need those files, Steve, so I can check them myself.
Bob
On Fri, Jan 30, 2009 at 8:33 AM, Stephen Hillier
wrote:
> Angel,
>
> thank you this is useful for me to understand how to load mutiple unit cells,
> but as you will see from my last post I think there is something else th
Jaim, I also suggest using
write isosurface ".jvxl"
from the Jmol application or signed applet. This only works if you
have a predefined notion of the surface you want to display; see notes
at
http://chemapps.stolaf.edu/jmol/docs/examples-11/isosurface.htm
and
http://chemapps.stolaf.edu/jm
Angel,
thank you this is useful for me to understand how to load mutiple unit cells,
but as you will see from my last post I think there is something else that has
confused me as well, because different CIF files for the same mineral from
reliable sources all appear to produce quite different r
Since my last reply I have tried loading some other CIf files for the
mineral Dickite from two sources (Am Min online database and ICSD)
Only one of the CIF files I have tried appears to behave as I would
expect, all the others appear to place atoms at incorrect positions,
indeed, in all but the o
Steve, It sees to me that instead of
"RELOAD {444 666 1}"
what you want may be the next menu entry,
"RELOAD {444 666 1}; display 555;"
Is it so?
And this is what these menu entries do, respectively:
save orientation; load "" {444 666 1} ; restore orientation; center;
and
save orientation; load
In settings other than Proteopedia I reduce the time required to display a
surface by generating a data file of the surface, and then just display the
surface rather than calculate the surface each time the script is run. I do
not think that there is a way to do this in Proteopedia, at least I hav
Jaime, I was writing a post for the Proteopedia list explaining just
this. Here is my advice:
I haven't looked at the source code, but this may help:
the sensible thing for pre-programmed surfaces in web pages is to
have Jmol save them as jvxl files, then make the page load that file -
- much fa
Paul,
thank you for the description of the display command, I assumed there
was some short hand way of displaying the range of cells, so I guess
that was one of my mistakes.
Bob,
the CIF file from the Am Min database is reproduced below,
I open it in the application and then I use the pop up m
There might be a cleverer way, but you can do :
display cell={2 2 2 } or cell={2 2 3 } or cell={2 2 4 } or cell={2 3
2 } or cell={2 3 3 } or cell={2 3 4 } or cell={2 4 2 } or cell={2 4
3 } or cell={2 4 4 } or cell={3 2 2 } or cell={3 2 3 } or cell={3 2
4 } or cell={3 3 2 } or cell={3 3 3 } o
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