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## jmol-users

 [Jmol-users] Finding all (symmetry-generated) symmetry elements in a unit cell From: Dean Johnston - 2011-04-21 15:45:27 Attachments: Message as HTML ```Does anybody know if there is a relatively simple way to find all the crystallographic symmetry elements within a unit cell using Jmol? For example, if there is an inversion center at the origin, there may be several other inversion centers generated by the space group symmetry. I can "see" some of them by asking Jmol for the symmetry relationship(s) between two atoms or two molecules. But I'm interested in generating a list of all the inversion centers (or glide planes, etc.) within the cell. Thanks for any insights. Dean ```
 Re: [Jmol-users] Finding all (symmetry-generated) symmetry elements in a unit cell From: Robert Hanson - 2011-04-21 16:16:02 Attachments: Message as HTML ```Dean, Well, it's just the product of all the symmetry operators. Get the collection of symmetry operators and multiply them until you get a complete set. I'll have to think about whether you can get all those as variables.... Yes, I think you can. You would have to normalize them to stay within the unit cell. strsymops = getproperty("auxiliaryinfo.models[1].symmetryOperations") print strsymops.length op = [] for (var i = 1; i < strsymops.length; i++) { op[i] = symop(i) print "" + strsymops[i] + "\n" + op[i] } op is then an array of the matrices, and you can multiply these at will. The problem you might have is whether there is a simple way to limit this to "within" the unit cell. For that, it's probably just as well to take a random point and keep operating on it, returning its unit cell coordinates each time. Anyway, since you can get the matrices for the space group operations, you should be able to get all combinations of them. Bob On Thu, Apr 21, 2011 at 10:45 AM, Dean Johnston wrote: > Does anybody know if there is a relatively simple way to find all the > crystallographic symmetry elements within a unit cell using Jmol? For > example, if there is an inversion center at the origin, there may be several > other inversion centers generated by the space group symmetry. I can "see" > some of them by asking Jmol for the symmetry relationship(s) between two > atoms or two molecules. But I'm interested in generating a list of all the > inversion centers (or glide planes, etc.) within the cell. Thanks for any > insights. > > Dean > > > ------------------------------------------------------------------------------ > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > 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 ```
 Re: [Jmol-users] Finding all (symmetry-generated) symmetry elements in a unit cell From: Dean Johnston - 2011-04-21 17:23:31 Attachments: Message as HTML ```OK - something along those lines was what I was thinking - thanks for the code example. Dean On Thu, Apr 21, 2011 at 12:15 PM, Robert Hanson wrote: > Dean, > > Well, it's just the product of all the symmetry operators. Get the > collection of symmetry operators and multiply them until you get a complete > set. I'll have to think about whether you can get all those as variables.... > Yes, I think you can. You would have to normalize them to stay within the > unit cell. > > strsymops = getproperty("auxiliaryinfo.models[1].symmetryOperations") > print strsymops.length > op = [] > > for (var i = 1; i < strsymops.length; i++) { > op[i] = symop(i) > print "" + strsymops[i] + "\n" + op[i] > } > > op is then an array of the matrices, and you can multiply these at will. > > The problem you might have is whether there is a simple way to limit this > to "within" the unit cell. For that, it's probably just as well to take a > random point and keep operating on it, returning its unit cell coordinates > each time. Anyway, since you can get the matrices for the space group > operations, you should be able to get all combinations of them. > > Bob > > On Thu, Apr 21, 2011 at 10:45 AM, Dean Johnston wrote: > >> Does anybody know if there is a relatively simple way to find all the >> crystallographic symmetry elements within a unit cell using Jmol? For >> example, if there is an inversion center at the origin, there may be several >> other inversion centers generated by the space group symmetry. I can "see" >> some of them by asking Jmol for the symmetry relationship(s) between two >> atoms or two molecules. But I'm interested in generating a list of all the >> inversion centers (or glide planes, etc.) within the cell. Thanks for any >> insights. >> >> Dean >> >> >> ------------------------------------------------------------------------------ >> Benefiting from Server Virtualization: Beyond Initial Workload >> Consolidation -- Increasing the use of server virtualization is a top >> priority.Virtualization can reduce costs, simplify management, and improve >> application availability and disaster protection. Learn more about >> boosting >> the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@... >> 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 > > > ------------------------------------------------------------------------------ > Benefiting from Server Virtualization: Beyond Initial Workload > Consolidation -- Increasing the use of server virtualization is a top > priority.Virtualization can reduce costs, simplify management, and improve > application availability and disaster protection. Learn more about boosting > the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev > _______________________________________________ > Jmol-users mailing list > Jmol-users@... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > ```