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 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 <[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 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 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> 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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Thank you. >> Macaulay Institute and Associated Companies, Macaulay Drive, >> Craigiebuckler, Aberdeen, AB15 8QH. >> >> >> ---------------------------------------------------------------------- > >> -------- >> This SF.net email is sponsored by: >> SourcForge Community >> SourceForge wants to tell your story. >> http://p.sf.net/sfu/sf-spreadtheword >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge CommunitJmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > 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. > Macaulay Institute and Associated Companies, Macaulay Drive, > Craigiebuckler, Aberdeen, AB15 8QH. > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > SourcForge Community > SourceForge wants to tell your story. > http://p.sf.net/sfu/sf-spreadtheword > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. 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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. Macaulay Institute and Associated Companies, Macaulay Drive, Craigiebuckler, Aberdeen, AB15 8QH. ------------------------------------------------------------------------------ This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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. 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