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Re: [Jmol-users] loading multiple unit cells and CIF files
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From: Robert H. <ha...@st...> - 2009-01-30 14:27:03
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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.H...@ma...> 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.H...@ma...> 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 <ha...@st...> 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.H...@ma...> 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 <pau...@ac...> 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. 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 >>> Jmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> >> > ------------------------------------------------------------------------------ >> This SF.net email is sponsored by: >> SourcForge CommunitJmol-users mailing list >> Jmo...@li... >> 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 >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> > > > > -- > 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 > > ------------------------------------------------------------------------------ > 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 > Jmo...@li... > 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 > Jmo...@li... > 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 > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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 |
