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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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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
