Steve, I'm still not seeing the problem. Attached is a JPG that looks
right to me.
Q: Does that look right to you?
Q: Does yours look different?
Q: Does the structure look wrong to you when you use the Jmol applet
at the Am Min site?
Q: Does it look wrong if you use:
load "http://rruff.geo.arizona.edu/AMS/xtal_data/CIFfiles/00124.cif" {1 1 1}
?
I would be very surprised if Jmol is incorrect in those structures.
Please just reiterate for me:
-- version of Jmol you are using
-- attach file contents, please
-- perhaps send a JPG of what you think is wrong
On Fri, Jan 30, 2009 at 8:15 AM, Stephen Hillier
<S.Hillier@...> wrote:
> Since my last reply I have tried loading some other CIf files for the
> mineral Dickite from two sources (Am Min online database and ICSD)
>
> Only one of the CIF files I have tried appears to behave as I would
> expect, all the others appear to place atoms at incorrect positions,
> indeed, in all but the one file that loads correctly, it is clear that
> the structure displayed is not the structure of Dickite.
>
>
> To my non crystallographic eye the space group and symmetry information
> in the CIF files I have tested all appear to be identical. Some of the
> files have data for hydrogen atom positions some not, and there are of
> course difference in the positions of atoms, but otherwise I can see no
> reason why they load to produce different and in most cases incorrect
> structures.
>
>
> If anyone would like to test this further I can supply some of the CIF
> files I have been using, I wasn''t sure it was acceptable practice to
> attach them to a mail to the list.
>
>
> sincerely,
>
>
> steve
>
>
>
>
>>>> "Stephen Hillier" <S.Hillier@...> 30-Jan-09 9:57 am >>>
> Paul,
>
> thank you for the description of the display command, I assumed there
> was some short hand way of displaying the range of cells, so I guess
> that was one of my mistakes.
>
> Bob,
>
> the CIF file from the Am Min database is reproduced below,
>
> I open it in the application and then I use the pop up menu command
> under the symmetry heading "Reload {444 666 1}"
>
> Then viewed from the "Right"
>
> there are two planes of oxygen atoms that are on their own, I
> wouldn't
> expect to see the plane that is furthest to the left in this view,
> also
> on the right hand side it is clear that planes of oxygen are missing,
> planes that form part of the silica tetrahedral. Also there are
> lonely
> OH's above and the below the main body of atoms in this view, I
> wouldn't expect them to be there either.
>
> many thanks
> steve
>
>
> data_global
> _chemical_name 'Dickite'
> loop_
> _publ_author_name
> 'Dera P'
> 'Prewitt C T'
> 'Japel S'
> 'Bish D L'
> 'Johnston C T'
> _journal_name_full "American Mineralogist"
> _journal_volume 88
> _journal_year 2003
> _journal_page_first 1428
> _journal_page_last 1435
> _publ_section_title
> ;
> Pressure-controlled polytypism in hydrous layered materials
> Sample: Low pressure dickite at P = 0.1 MPa
> ;
> _chemical_formula_sum 'Si2 Al2 O9 H4'
> _cell_length_a 5.161
> _cell_length_b 8.960
> _cell_length_c 14.459
> _cell_angle_alpha 90
> _cell_angle_beta 96.77
> _cell_angle_gamma 90
> _cell_volume 663.959
> _symmetry_space_group_name_H-M 'C 1 c 1'
> loop_
> _symmetry_equiv_pos_as_xyz
> 'x,y,z'
> '1/2+x,1/2+y,z'
> 'x,-y,1/2+z'
> '1/2+x,1/2-y,1/2+z'
> loop_
> _atom_site_label
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> _atom_site_Uiso_or_equiv
> Si1 0.00880 0.40100 0.03240 0.01200
> Si2 -0.00350 0.07220 0.03150 0.01000
> Al1 0.91260 0.25230 0.22330 0.01600
> Al2 0.41840 0.41760 0.22260 0.01800
> O1 0.95620 0.23800 0.98640 0.01700
> O2 0.25480 0.47140 0.98560 0.01800
> O3 0.76360 0.50580 0.99910 0.01700
> O4 0.07890 0.39080 0.14280 0.02100
> O5 0.00250 0.08070 0.14430 0.01200
> O-h1 0.58500 0.27470 0.14880 0.02200
> O-h2 0.24320 0.27800 0.28660 0.01800
> O-h3 0.25250 0.89320 0.28880 0.01500
> O-h4 0.32340 0.58370 0.28630 0.02100
> H1 0.57000 0.17300 0.15200 0.02600
> H2 0.30700 0.26000 0.34600 0.02200
> H3 0.25000 0.99000 0.30500 0.01800
> H4 0.27000 0.58800 0.34200 0.02600
>
>
>
>>>> Robert Hanson <hansonr@...> 29-Jan-09 11:17 pm >>>
> please send that file, and perhaps a description of what you would
> expect to see instead of what you see.
>
> Bob
>
>
> On Thu, Jan 29, 2009 at 3:47 PM, Stephen Hillier
> <S.Hillier@...> wrote:
>> 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 <paul.pillot@...> 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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>
>
> --
> 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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> copy, disclose or rely on any information contained in this e-mail,
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> we would ask you to contact the sender immediately and delete the
> email
> from your system. Thank you.
> Macaulay Institute and Associated Companies, Macaulay Drive,
> Craigiebuckler, Aberdeen, AB15 8QH.
>
>
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>
>
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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
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