Egon Willighagen wrote:
load quartz.cif;set showUnitCell on
# standard load reads only the file data -- no symmetry applied
load "quartz.cif" {2 2 2};set showUnitCell on
# note that quotation marks REQUIRED when the number of unit cells
is given
This cannot be split up this in steps:
1. apply symmetry operations
2. apply lattice growing
So, something like:
load quartz.cif; set showUnitCell on
set spacegroup p1
[oooh, you want to be able to specify DIFFERENT space groups. Now THAT
would be interesting....]
# to apply the symmetry operations
set spacegroup original
set lattice {2 2 2}
because the growing has to be done on loading, right?
Yes, for now at least. I didn't feel like being so extreme as to also
mess with adding atoms after loading. I'm not convinced that that can be
done successfully.
load calcite.cif;set showUnitCell on
load "calcite.cif" {3 2 1};set showUnitCell on
load maleic.cif;set showUnitCell on
load "maleic.cif" {1,1,1};set showUnitCell on
What is the meaning of the ',' in the lattice specification?
just optional -- coordinates are expressible with or without the commas
in all the prototype applications (centering, drawing, rotating,
spinning) using molecular coordinates. I'm thinking about how to
designate fractional coordinates. What do you think of this:
{1/2, 1/3, 1/3}
In other words, the "fraction" sign for "fractional" coordinates. The
numbers wouldn't have to be integers -- you could use:
{0.5/1, 0.333/1, 0.333/1}
or just
{0.5/, 0.333/, 0.333/}
as well. ("1" would be implied as the denominator.)
How does that sound for "fractional coordinates"?
BTW, Jmol 9 supported a range, instead of an integer. For example, 0,0,0
was the unit cell, so negative numbers would grow in one direction while
positive numbers would grow in the other direction. So, {-1,1; -1,1; -1,1}
would create a 3x3x3 lattice, with the original unit cell in the center.
That could be more difficult because it uses the line-end semicolon.
I can't see why that would be important. All unit cells are the same. Or
is it just the idea of centering?
Tell me if you think it's really important. I'm not allowing any
negative numbers here, but it's not out of the question, I guess..
# note that this file has 18 models, each with a different unit cell
OK, is sort of what I expected but not quite. I would suggest to either:
1. show only the atoms of this unit cell in connected manner, or
2. show only the atoms that physically are in the unit cell box, which
would break connectivity.
What you see there is just what the 10.2 CIF reader displays right now
-- the CIF data, untouched. I thought the friendliest modification would
be to make it so what you see with no qualifiers is the same as in 10.2.
Presumably SOMEONE thinks this is what one should see.
Now it does a bit of both, which is confusing.
Hmm. This is just the way the data are in that CIF file. What makes it
"confusing" for you? Maybe you could get used to it? :)
I like the selection of the frame number. Is that new too?
Yes. This could be extended easily to any file reader, because the way I
set it up it works generically - not special to CIF. The idea would be:
load "filename" [model#]
(The quotes are necessary so as to allow for complex filenames.) It
seems to me this could be quite generally useful.Why read the whole file
if you have the desired model already in hand? An easy addition that I
think just hasn't been thought of before.
Bob
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