Pat,
You're in luck. The following will be available in the next prerelease
(10.9.77):
load "filename" {ijk i'j'k' doNormalize}
where
ijk and i'j'k' are the cell designations of the two corner cells in
the block, which should include 555.
doNormalize = 1 for standard geometric-center normalization into the
unit cell
doNormalize = 0 for respecting the exact form of the Jones Faithful terms
For example:
load "" {444 666 1}
would be a popular option, loading all the cells around 555 and
normalizing all the symmetry operations.
load "" {555 555 0}
loads all the symmetry for one unit cell exactly as designated in the
file, with no normalization. So if in the file you have a Jones Faithful
designation as crazy as
x-1.25 -y-5/6 z
that is exactly what will be used.
You can use
show symmetry
to see exactly what operators were used.
Also, note that the load command can take a list of Jones Faithful
operators that will override anything in the file:
load "myfile" {444 666 0} spacegroup "x,y,z;x-1.25,-y-5/6, z"
So you can use that for illustration or experimenting with symmetry
operators.
By the way, simplest way to get the symmetry list is:
var info = jmolScriptWaitAsArray("show symmetry")[0][0][3]
([0] first messagetype (scriptEcho) -- [0] first message -- [3]value)
which delivers:
Symmetry Information:|model #1; name=global|Spacegroup: P 32 2 1|Number
of symmetry operations: 6|Symmetry
Operations:|x,y,z|y,x,-z-1/3|-y,x-y,z-1/3|-x,-x+y,-z+1/3|-x+y,-x,z+1/3|x-y,-y,-z
You can then use:
var Operators = info.split("|")
var op1 = Operators[4] // "x,y,z"
var op2 = Operators[5] // "y,x,-z-1/3"
....
up to
var opn = Operators[Operators.length - 1]
The first operator will ALWAYS be "x,y,z" regardless of what list is
provided in the file.
These are the operators exactly as described in the file when
doNormalize=0; cleaned up and standardized when doNormalize=1.
I expect very cool websites from you now....
Bob
P.J. Carroll wrote:
> I'm trying to compose a general web page that would allow
>users to construct a unit cell packing diagram using a CIF and
>whatever strategy they would like to pursue. My first attempt is at:
>
> http://macxray.chem.upenn.edu/cells/3159SG.html
>
>To develop this, tho, two changes would be nice:
>
>(1) right now, a symop, for example, -X, 1/2+Y, 1/2-Z, that would put
>a molecule in a neighboring unit cell with a negative X-coordinate is
>adjusted by Jmol so the co-ordinates are all positive. I would prefer
>that the symop -X, 1/2+Y, 1/2-Z actually put the molecule at a
>negative X! This is important if I have an external program that
>tells me there is a hydrogen bond between symop X, Y, Z and symop -X,
>1/2+Y, 1/2-Z. I would like to be able to draw those specific
>molecules with Jmol.
>
>(2) could the command load "" {3 3 3} be changed to also accommodate
>negative co-ordinates? That is instead of loading cells 555 thru 777
>with 555 being the base cell, it would be nice if it loaded cells 444
>thru 666 with 555 being the base cell. Again, this change would make
>Jmol agreeable with other output that has, e.g., a hydrogen bond to a
>molecule at -1+X, 1/2-Y, 1/2+Z.
>
>And finally that page referenced above was written for space group
>P2(1)/c and those four specific symops. Is it possible to communicate
>from the CIF the number of symops and their x, y, z expressions so a
>general page could be written that does not know the symops
>beforehand? Is this something that can be done by javascript?
>
>
>Pat Carroll
>Chem Dept
>U of Penn
>
>
>
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-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
_______________________________________________
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