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