On Fri, Apr 1, 2011 at 9:58 AM, Pshemak Maslak <p...@chem.psu.edu> wrote:
> On 4/1/2011 10:18 AM, Robert Hanson wrote:
>
>
>
> On Fri, Apr 1, 2011 at 9:10 AM, Pshemak Maslak <p...@chem.psu.edu> wrote:
>
> My questions:
>>
>> Where is the connectivity information in that file? The Jmol shows the
>> nice tetrahedron "subunits" {1,1,1} with "bonds" between atoms. Is that
>> based on proximity of these atoms?
>>
>>
> exactly
>
> That would mean that Jmol has maximum bonding distances stored for all
> element combinations. Is that correct?
>
>
It does, and it doesn't always work properly for all metals. So you may have
to do some
connect
commands for a given specific case to get it exactly the way you want it.
> I like the brevity of that file format. Is there a good source of cif files
> for (crystalline) elements somewhere?
>
I like the American Mineralogist site at
http://rruff.geo.arizona.edu/AMS/amcsd.php
> This would help to avoid "manual" mistakes and cases where origins are not
> at 0,0,0. What do you mean by "problems with settings"?
>
>
Some space groups have different settings, meaning they have the same name
but different symmetry operations. Shouldn't be a problem with Hall names, I
think.
> Can one "invent" unit cells for "hypothetical" atoms or does the atom size
> (stored in Jmol?) and cell dimensions have to be consistent?
>
> Thanks for your help,
>
>
You can do anything you want. And check the crystallographic options for
LOAD. You can over-ride any of the space group, symmetry operator, or unit
cell information in a CIF file from the LOAD command line.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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