## jmol-users

 [Jmol-users] Viewing unit cells down crystallographic axes From: Brian McMahon - 2009-07-01 15:40:58 ```Is there a neat way (perhaps using quaternions) to view a triclinic unit cell down its crystallographic axes? i.e. a moveto command so that the cell ends up with its c axis normal to the screen and its ac face (in projection) lying horizontally? Thanks Brian ```
 Re: [Jmol-users] Viewing unit cells down crystallographic axes From: Robert Hanson - 2009-07-01 16:21:26 Attachments: Message as HTML ```I think it's just angles and cross products: var axisC = {0 0 1/1 } var axisZ = {0 0 1} rotAxis = cross(axisZ,axisC) rotAngle = angle(axisZ, {0 0 0},rotAxis, axisC) draw {0 0 0} @{rotAxis * 10} print " " + rotAngle + " " + rotAxis reset rotate molecular {0 0 0} @rotAxis @rotAngle The cross product gets you an axis perpendicular to the other two. That trick with the rotAngle done as a dihedral gets you a directed angle rather than just a positive value for which you don't know which way to turn. Then you can work out how you want to rotate the others. I'll leave that as a puzzle for you. Bob On Wed, Jul 1, 2009 at 10:40 AM, Brian McMahon wrote: > Is there a neat way (perhaps using quaternions) to view a triclinic > unit cell down its crystallographic axes? i.e. a moveto command so > that the cell ends up with its c axis normal to the screen and its > ac face (in projection) lying horizontally? > > Thanks > Brian > > > ------------------------------------------------------------------------------ > _______________________________________________ > 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] Viewing unit cells down crystallographic axes From: Brian McMahon - 2009-07-01 16:47:00 ```Bob Neat indeed! This in itself is a great didactic tool for demonstrating rotational transformations. > I'll leave that as a puzzle for you. I'll cheerfully pass it on to my summer student! Many thanks again, Brian > I think it's just angles and cross products: > > var axisC = {0 0 1/1 } > var axisZ = {0 0 1} > rotAxis = cross(axisZ,axisC) > rotAngle = angle(axisZ, {0 0 0},rotAxis, axisC) > draw {0 0 0} @{rotAxis * 10} > print " " + rotAngle + " " + rotAxis > reset > rotate molecular {0 0 0} @rotAxis @rotAngle > > The cross product gets you an axis perpendicular to the other two. > That trick with the rotAngle done as a dihedral gets you a directed angle > rather than just a positive value for which you don't know which way to > turn. > > Then you can work out how you want to rotate the others. I'll leave that as > a puzzle for you. > > Bob > > On Wed, Jul 1, 2009 at 10:40 AM, Brian McMahon wrote: > > > Is there a neat way (perhaps using quaternions) to view a triclinic > > unit cell down its crystallographic axes? i.e. a moveto command so > > that the cell ends up with its c axis normal to the screen and its > > ac face (in projection) lying horizontally? > > > > Thanks > > Brian > -- > 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 _________________________________________________________________________ Brian McMahon tel: +44 1244 342878 Research and Development Officer fax: +44 1244 314888 International Union of Crystallography e-mail: bm@... 5 Abbey Square, Chester CH1 2HU, England ```