Steve,
Besides the fact that you found some apparently incorrect data in one
of the CIF files, your initial question relating to the oxygens and
other atoms oddly displaced has to do with the way Jmol applies the
symmetry operators. In some cases, as you see there, just loading a
single unit cell may displace atoms in an unexpected way.
So, thinking about that, I've made a little addition to the load
options. Jmol 11.7.23 adds the "-1" option to unit cell loading. This
option forces full packing of the unit cell, which in some cases may
be preferable to the 0 (unnormalized) or 1 (normalized) options.
So, now you can do, for example:
load "dickite.cif" {555 555 -1}
and those oxygens will be moved into the unit cell.
You can check this out at
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
http://chemapps.stolaf.edu/jmol/docs?command=load
The new Jmol.jar file is included there as part of Jmol-11.zip.
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. 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
>
>
> ------------------------------------------------------------------------------
> 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. 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
