## jmol-users

 [Jmol-users] Problem with unit cell in Jmol 11.0 From: P.J. Carroll - 2006-08-30 23:57:47 ```I have a CIF of a metal complex in which the metal is on a crystallographic center of symmetry. Thus the CIF only contains co-ordinates of half a molecule and the symmetry position -x, -y, -z should produce the second half. When I do a load "" {1 1 1}, this second half is not produced. It finally is with a load "" {2 2 2}. To see what I'm talking about, take a look at: http://macxray.chem.upenn.edu/cells/938cell.html I assume it has something to do with the co-ordinates of all the atoms in that second half being negative (which, then, when translated +1, +1, +1 should end up in the center of the original unit cell). Pat ```
 Re: [Jmol-users] Problem with unit cell in Jmol 11.0 From: Bob Hanson - 2006-08-31 00:18:56 ```use load "test.cif" {2 2 2};restrict molecule=1 This is a general way to ensure that your molecules are complete Bob P.J. Carroll wrote: >I have a CIF of a metal complex in which the metal is on a >crystallographic center of symmetry. Thus the CIF only contains >co-ordinates of half a molecule and the symmetry position -x, -y, -z >should produce the second half. When I do a load "" {1 1 1}, this >second half is not produced. It finally is with a load "" {2 2 2}. > >To see what I'm talking about, take a look at: > > http://macxray.chem.upenn.edu/cells/938cell.html > >I assume it has something to do with the co-ordinates of all the >atoms in that second half being negative (which, then, when >translated +1, +1, +1 should end up in the center of the original >unit cell). > > > >Pat > > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ```
 Re: [Jmol-users] Problem with unit cell in Jmol 11.0 From: Bob Hanson - 2006-09-12 14:13:38 ```Pat, I finally got around to checking on http://macxray.chem.upenn.edu/cells/cifs/938.cif. The problem is a general one: Jmol always shifts the geometric center of symmetry-generated points into the unit cell. This was the key to making symmetry operators work well. However, Jmol does not alter the original file positions. In the case where the geometric center of the file coordinates lies outside the unit cell (as in this case), those coordinates are "left behind". But I have an idea.... Bob P.J. Carroll wrote: >I have a CIF of a metal complex in which the metal is on a >crystallographic center of symmetry. Thus the CIF only contains >co-ordinates of half a molecule and the symmetry position -x, -y, -z >should produce the second half. When I do a load "" {1 1 1}, this >second half is not produced. It finally is with a load "" {2 2 2}. > >To see what I'm talking about, take a look at: > > http://macxray.chem.upenn.edu/cells/938cell.html > >I assume it has something to do with the co-ordinates of all the >atoms in that second half being negative (which, then, when >translated +1, +1, +1 should end up in the center of the original >unit cell). > > > >Pat > > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ```
 Re: [Jmol-users] Problem with unit cell in Jmol 11.0 From: Bob Hanson - 2006-09-12 14:53:55 ```OK, the latest upload includes: translateSelected {x y z} This command moves atoms RELATIVE to the other atoms. So, Pat, if you like, you can use select symop=1 #always the original points translateSelected {0 0 -1/1} thus moving that molecule back into the unit cell. Or, if you prefer, select symop=2 translateSelected {0 0 1/1} which would move the other molecule in. Have fun. Bob P.J. Carroll wrote: >I have a CIF of a metal complex in which the metal is on a >crystallographic center of symmetry. Thus the CIF only contains >co-ordinates of half a molecule and the symmetry position -x, -y, -z >should produce the second half. When I do a load "" {1 1 1}, this >second half is not produced. It finally is with a load "" {2 2 2}. > >To see what I'm talking about, take a look at: > > http://macxray.chem.upenn.edu/cells/938cell.html > >I assume it has something to do with the co-ordinates of all the >atoms in that second half being negative (which, then, when >translated +1, +1, +1 should end up in the center of the original >unit cell). > > > >Pat > > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmol-users@... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ```