There might be a cleverer way, but you can do :
display cell={2 2 2 } or cell={2 2 3 } or cell={2 2 4 } or cell={2 3
2 } or cell={2 3 3 } or cell={2 3 4 } or cell={2 4 2 } or cell={2 4
3 } or cell={2 4 4 } or cell={3 2 2 } or cell={3 2 3 } or cell={3 2
4 } or cell={3 3 2 } or cell={3 3 3 } or cell={3 3 4 } or cell={3 4
2 } or cell={3 4 3 } or cell={3 4 4 } or cell={4 2 2 } or cell={4 2
3 } or cell={4 2 4 } or cell={4 3 2 } or cell={4 3 3 } or cell={4 3
4 } or cell={4 4 2 } or cell={4 4 3 } or cell={4 4 4 }
-Paul
Le 29 janv. 09 à 22:47, Stephen Hillier a écrit :
> Paul,
>
> thank you for you help, in the example I gave I appear to have whole
> planes of oxygens in the wrong place.
>
> However the central portion of the block looks like it might have all
> the atoms in the correct place.
>
> I know how to load a block of 5 by 5 by 5 cells, but I haven't
> manged to
> figure out how to display the central block of 27
>
> Can you give me an example?
>
> thank you,
>
> steve
>
>
>
>>>> Paul Pillot <[email protected]> 01/29/09 3:52 PM >>>
> I think the display you get is normal. The "orphan atoms" you have on
> the boundary of unitcells are connected to atoms in nearby unitcells.
> When you load 3x3x3 unitcells, only the central one is whole. If you
> want to display only this unitcell, use the command :
> display cell={2 2 2}
> So if you want to see 3x3x3 whole unitcells, you should load 5x5x5
> unitcells and only display the 27 central ones...
> Paul
>
> Le 29 janv. 09 à 14:26, Stephen Hillier a écrit :
>
>> A question from a novice, trying to learn to use Jmol.
>>
>> I have been trying to load CIF files into Jmol and display ranges
>> of unit cells,
>>
>> I don't currently understand all the options for doing this but I
>> also get some results that appear to me to be a little strange?
>>
>> I have tried loading examples of CIF files from the American
>> Mineralogist Crystal Structure database.
>>
>> http://rruff.geo.arizona.edu/AMS/amcsd.php
>>
>> For example, I downloaded the structure in CIF format for the
>> mineral Dickite (the low pressure one by Dera et al, No 03168 in
>> the database)
>>
>>
>> I open this file in the Jmol application,
>>
>> and then reload it with the popup menu command labelled "RELOAD
>> {444 666 1}"
>>
>> My understanding of this command was that it loads a block of unit
>> cells.
>>
>> However in the resulting model displayed there are two lonely
>> planes of oxygen atoms out on their own, and also a number of atoms
>> around the edge of the model all of which look like they are out of
>> place.
>>
>>
>> I have tried a CIF file for exactly the same structure from another
>> source and get an identical result, and I get similar results with
>> other CIF files for other minerals.
>>
>>
>> Any advice on what I may be doing incorrectly, or how to get these
>> structures to load blocks of unitcells correctly would be much
>> appreciated.
>>
>> I don't fully understand the various ways of loading cell ranges,
>> so I guess that could be the problem, so any basic explanations of
>> the sorts of commands that can be used would also be appreciated.
>>
>> I wondered if it might be something to do with the symmetry
>> operations in the CIF file not being interpreted correctly, but I'm
>> not a crsytallographer so I need some help to put me on the right
>> track.
>>
>> sincerely,
>>
>>
>> steve
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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