{1 1 1} replicates the symmetry operations, and some of those might bring
an atom into another unit cell. Particularly with molecular compounds, we
see this all the time, and it is what people want.
You can specify PACKED to get only atoms within one unit cell, although
then atoms that are at vertices or on faces of the unit cell are
duplicated. You could try that. PACKED by itself implies {1 1 1} PACKED:
load t.pdb PACKED
load t.pdb {2 2 2} PACKED
But I'm guessing you will not like that!
Would you say the same about the atoms on the edges? They are in other unit
cells as well.
There's probably no adequate solution I can offer you.
Bob
On Wed, Nov 30, 2011 at 11:35 AM, Hans Horn <[email protected]> wrote:
> Bob,
>
> whatever magic you did - it fixed the atom duplication.
> However, I think the unit cell should have only 9 atoms, not 10.
>
>
>
> The Mg atom (0.0 0.0 17.59) pointed to by the arrow should be in the
> next cell, shouldn't it?.
>
> I'm afraid that I did not catch the meaning of what I should do about
> "REMARK 290".
>
> Anyhow, thank you very much for this incredibly fast turn around.
>
> Are you going to release your fix soon?
>
> Greets,
> Hans
>
>
> On 11/29/2011 8:09 PM, Robert Hanson wrote:
>
> Hans,
>
> OK, I got it. Very simple fix. See
> http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip
>
> By the way, Jmol is guessing at the origin and setting of that unit cell.
> Jmol can read the Jones-Faithful data in the PDB record REMARK 290:
>
> REMARK 290 CRYSTALLOGRAPHIC
> SYMMETRY
> REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21
> 1
> REMARK
> 290
> REMARK 290 SYMOP
> SYMMETRY
> REMARK 290 NNNMMM
> OPERATOR
> REMARK 290 1555
> X,Y,Z
> REMARK 290 2555
> -X,Y+1/2,-Z
> REMARK
> 290
>
> That's guaranteed to work.
>
> Bob Hanson
>
>
>
>
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>
--
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
<<ebgcbibi.png>>
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