Bob, the new load option certainly helps a lot. The atoms in apparently odd positions and the fact that one CIF I chose turned out to have a typo resulting in a silicon in the wrong place - all contributed to make a confusing picture for me.
In answer to your questions below A: yes your jpg file of the structure looks correct A: No the structure I get is exactly the same for this CIF file A: No at the Am Min site for this CIF file the structure looks fine, i.e the file of the Dickite structure determined by Bailey 1963 A: No it still looks fine If I load this CIF using this URL. The version of Jmol I was using is 11.6.8 Having looked carefully at all the CIF files for this mineral again I think I know what has confused me. Looking at the Bailey structure (i.e 00124 at the Am Min site) the sheets of siilca tetrahedra are superimposed (i,e they line up) when you look down C, the easiest way to see this is making them into polyhedra. This view is identical to the view that you see in the mineral kaolinite and the kaolinite and dickite structure only differ in the details of where aluminim atoms are placed in the octahedral sheet. So the Bailey structure in CIF 00124 is what I was expecting to see, i.e it looks like kaolinite except for the difference in the octahedral sheet. With all the other CIF file of dickite that I looked at (Am Min and ICSD) the sheets of silicate tetrahedra do not line up with each other when you look down C. However, If you ignore the unit cell ouline that is shown you can tilt the structure into a view that is like the one I was expecting. I also note that the monoclinic angle in the Bailey structure is much larger than in all the other examples - so I think the reason it 'looks' wrong in the other files is because of this difference in the unit cell? As least I think this is the explanation? sincerely, steve >>> Robert Hanson <[email protected]> 01/31/09 10:16 PM >>> 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 <[email protected]> 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" <[email protected]> 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 t> 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 <[email protected]> 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 > <[email protected]> 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 <[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 >>> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> Please note that the views expressed in this e-mail are those of > the >>> sender and do not necessarily represent the views of the Macaulay >>> Institute. 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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 -- Please note that the views expressed in this e-mail are those of the sender and do not necessarily represent the views of the Macaulay Institute. This email and any attachments are confidential and are intended solely for the use of the recipient(s) to whom they are addressed. If you are not the intended recipient, you should not read, copy, disclose or rely on any information contained in this e-mail, and we would ask you to contact the sender immediately and delete the email from your system. Thank you. 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