Re: [Jmol-users] Re: crystal structures and symmetry

[Bob H. <ha...@st...>]

OK, that sounds interesting. To date with the prototype at 
http://www.stolaf.edu/people/hansonr/jmol/test/proto/sym.htm
You can:

-load CIF files with or without application of symmetry

load "myfile.cif"

-load CIF files containing more than one data record

same

-load a SPECIFIC data record from a multiple-model CIF file

load "myfile.cif" 3

-load a given number of unit cells in the a, b, and c directions:

load "myfile.cif" {1,2,3}

(I'm looking for comments about those packings)

-turn the cell parameter display on and off:

set displayUnitcellParameters ON/OFF

-set the axes to be those of the unit cell and turn them on and off:

set axesUnitCell ON/OFF
set axes ON/OFF

-use the mouse to select specific molecules:

set picking molecule

-select an atom's molecule:

select within(molecule, atomno=1)

Of course, connect those hydrogen bonds:

connect 1.2 2.4 (hydrogen) (oxygen) hbonds create

(or something to that effect)

I'll take a look at the SHELX/LATT document.
In terms of adding molecules one at a time, this will be more like add 
them all, then turn them all off and selectively "add" them, meaning 
"display" them.
Should work!

Bob


P.J. Carroll wrote:

>     I agree with Egon that the inclusion of symmetry in Jmol would be 
> very useful to practicing crystallographers like myself. It could be 
> used to display and teach space group symmetry (take a look at 
> http://macxray.chem.upenn.edu/cells/cell457total.html) and to 
> investigate intermolecular attractions like hydrogen bonds (see 
> http://macxray.chem.upenn.edu/9178.html).
>     Also, to address a question about the LATT instruction in SHELXL, 
> I have prepared a PDF document that explains it 
> (http://macxray.chem.upenn.edu/LATT.pdf).
>     I would want the user to have as much control as possible. It 
> would be somewhat useful to have an option that just fills the unit 
> cell with the molecules, but each packing diagram investigation is 
> different and it would be desirable to be able to add a molecule at a 
> time by selecting a symmetry position and any necessary translations.
>
>
> Patrick J. Carroll
> Director, X-ray Facility
> Department of Chemistry
> University of Pennsylvania
> Philadelphia, PA
>
>
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