Re: [Jmol-users] Polyhedra with 12 or 20 vertices
OK, I see that the POLYHEDRA command is really overkill for what I'm trying to do. I could essentially create my own polyhedral representations if the DRAW command was extended to allow the drawing of planes with an arbitrary number of vertices so that I could create triangles, pentagons, etc. as needed. Should I submit this as a feature request??? Dean On 6/9/07 12:51 AM, Bob Hanson [EMAIL PROTECTED] wrote: Dean, sounds like you might appreciate: http://www.scienceu.com/geometry/facts/solids/coords/ Well, ah, let's just say it doesn't work the way you probably think it does. The polyhedra code is a very complex algorithm that looks at possible faces (combinations of three atoms around a central atom) and determines which are faces and which are not. We have: #atoms comb of 3 at a time 4 4!/(3!)(1!) = 4 6 6!/3!3! = 20 8 8!/3!5! = 56 9 9!/3!6! = 84 12 12!/3!9! = 220 20 20!/3!17! = 1140 ... n n(n-1)(n-2)/6 so if you do nothing special, then you will possibly run into the problem with any number more than 9. HOWEVER, the algorithm has a parameter, distanceFactor, that is adjustable, and if you set it smaller, it will work. For example (That second line should not wrap), try: 13 #jmolscript: connect (*) (*) delete;connect (_Fe) (_C);select *;wireframe off;spacefill off;select (_Fe); polyhedra bonds distanceFactor 0.5 Fe 0 0 0 C -0.692 0.000 0.427 C 0.000 0.427 -0.692 C 0.000 0.427 0.692 C 0.692 0.000 -0.427 C -0.427 -0.692 0.000 C -0.427 0.692 0.000 C 0.000 -0.427 0.692 C 0.427 0.692 0.000 C 0.000 -0.427 -0.692 C 0.692 0.000 0.427 C 0.427 -0.692 0.000 C -0.692 0.000 -0.427 As for dodecahedra, that's just too large. I've upped the maximum number of faces to 147, and that takes care of it, but there are a few stray lines, since we are painting more triangles than actually needed. Just the way it goes, I guess Bob Dean Johnston wrote: Has anybody tried to create polyhedra with 12 or 20 vertices? The documentation seems to indicate that I should be able to go up to 20. I¹m creating representations of shapes (Platonic solids, actually maybe Jmol isn¹t just for molecules anymore... :-). I would like to display an icosahedron and dodecahedron. I¹ve created structures with a central atom surrounded by 12 or 20 atoms, but when I try and create the polyhedron, I get the following error message: Polyhedron error: maximum face(87) -- reduce RADIUS I have a feeling it¹s creating more polyhedra faces than I want it to (I only want 20), but I¹m not entirely familiar with how it works. I¹ve gotten it to work just fine for tetrahedra and octahedra. Any insights, corrections, etc. are greatly appreciated. My testing page is at: http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/poly.html Dean - - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Polyhedra with 12 or 20 vertices
Dean Johnston wrote: OK, I see that the POLYHEDRA command is really overkill for what I'm trying to do. I could essentially create my own polyhedral representations if the DRAW command was extended to allow the drawing of planes with an arbitrary number of vertices so that I could create triangles, pentagons, etc. as needed. Should I submit this as a feature request??? Yes, but don't hold your breath. It isn't core Jmol to be drawing random objects. If you really want to do it with Jmol, think about ways you can do it yourself with Jmol and triangles/quadrilaterals, and you will get there faster. You can load a file of coordinates and work with it to draw just about anything you want, provided the objects are triangles or quadrilaterals. Pmesh is another command that comes to mind. Bob Dean On 6/9/07 12:51 AM, Bob Hanson [EMAIL PROTECTED] wrote: Dean, sounds like you might appreciate: http://www.scienceu.com/geometry/facts/solids/coords/ Well, ah, let's just say it doesn't work the way you probably think it does. The polyhedra code is a very complex algorithm that looks at possible faces (combinations of three atoms around a central atom) and determines which are faces and which are not. We have: #atoms comb of 3 at a time 4 4!/(3!)(1!) = 4 6 6!/3!3! = 20 8 8!/3!5! = 56 9 9!/3!6! = 84 12 12!/3!9! = 220 20 20!/3!17! = 1140 ... n n(n-1)(n-2)/6 so if you do nothing special, then you will possibly run into the problem with any number more than 9. HOWEVER, the algorithm has a parameter, distanceFactor, that is adjustable, and if you set it smaller, it will work. For example (That second line should not wrap), try: 13 #jmolscript: connect (*) (*) delete;connect (_Fe) (_C);select *;wireframe off;spacefill off;select (_Fe); polyhedra bonds distanceFactor 0.5 Fe 0 0 0 C -0.692 0.000 0.427 C 0.000 0.427 -0.692 C 0.000 0.427 0.692 C 0.692 0.000 -0.427 C -0.427 -0.692 0.000 C -0.427 0.692 0.000 C 0.000 -0.427 0.692 C 0.427 0.692 0.000 C 0.000 -0.427 -0.692 C 0.692 0.000 0.427 C 0.427 -0.692 0.000 C -0.692 0.000 -0.427 As for dodecahedra, that's just too large. I've upped the maximum number of faces to 147, and that takes care of it, but there are a few stray lines, since we are painting more triangles than actually needed. Just the way it goes, I guess Bob Dean Johnston wrote: Has anybody tried to create polyhedra with 12 or 20 vertices? The documentation seems to indicate that I should be able to go up to 20. I¹m creating representations of shapes (Platonic solids, actually ‹ maybe Jmol isn¹t just for molecules anymore... :-). I would like to display an icosahedron and dodecahedron. I¹ve created structures with a central atom surrounded by 12 or 20 atoms, but when I try and create the polyhedron, I get the following error message: Polyhedron error: maximum face(87) -- reduce RADIUS I have a feeling it¹s creating more polyhedra faces than I want it to (I only want 20), but I¹m not entirely familiar with how it works. I¹ve gotten it to work just fine for tetrahedra and octahedra. Any insights, corrections, etc. are greatly appreciated. My testing page is at: http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/poly.html Dean - - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Polyhedra with 12 or 20 vertices
On 6/13/07 12:38 PM, Bob Hanson [EMAIL PROTECTED] wrote: Yes, but don't hold your breath. It isn't core Jmol to be drawing random objects. If you really want to do it with Jmol, think about ways you can do it yourself with Jmol and triangles/quadrilaterals, and you will get there faster. You can load a file of coordinates and work with it to draw just about anything you want, provided the objects are triangles or quadrilaterals. Pmesh is another command that comes to mind. Bob Triangles and quadrilaterals will do just fine - for some reason I had the PLANE keyword in my DRAW commands, so I forgot that triangles were that easy. Thanks! Dean Dean Johnston wrote: OK, I see that the POLYHEDRA command is really overkill for what I'm trying to do. I could essentially create my own polyhedral representations if the DRAW command was extended to allow the drawing of planes with an arbitrary number of vertices so that I could create triangles, pentagons, etc. as needed. Should I submit this as a feature request??? - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Polyhedra with 12 or 20 vertices
Has anybody tried to create polyhedra with 12 or 20 vertices? The documentation seems to indicate that I should be able to go up to 20. I¹m creating representations of shapes (Platonic solids, actually maybe Jmol isn¹t just for molecules anymore... :-). I would like to display an icosahedron and dodecahedron. I¹ve created structures with a central atom surrounded by 12 or 20 atoms, but when I try and create the polyhedron, I get the following error message: Polyhedron error: maximum face(87) -- reduce RADIUS I have a feeling it¹s creating more polyhedra faces than I want it to (I only want 20), but I¹m not entirely familiar with how it works. I¹ve gotten it to work just fine for tetrahedra and octahedra. Any insights, corrections, etc. are greatly appreciated. My testing page is at: http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/poly.html Dean - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Polyhedra with 12 or 20 vertices
Dean, sounds like you might appreciate: http://www.scienceu.com/geometry/facts/solids/coords/ Well, ah, let's just say it doesn't work the way you probably think it does. The polyhedra code is a very complex algorithm that looks at possible faces (combinations of three atoms around a central atom) and determines which are faces and which are not. We have: #atoms comb of 3 at a time 4 4!/(3!)(1!) = 4 6 6!/3!3! = 20 8 8!/3!5! = 56 9 9!/3!6! = 84 12 12!/3!9! = 220 20 20!/3!17! = 1140 ... n n(n-1)(n-2)/6 so if you do nothing special, then you will possibly run into the problem with any number more than 9. HOWEVER, the algorithm has a parameter, distanceFactor, that is adjustable, and if you set it smaller, it will work. For example (That second line should not wrap), try: 13 #jmolscript: connect (*) (*) delete;connect (_Fe) (_C);select *;wireframe off;spacefill off;select (_Fe); polyhedra bonds distanceFactor 0.5 Fe 0 0 0 C -0.692 0.000 0.427 C 0.000 0.427 -0.692 C 0.000 0.427 0.692 C 0.692 0.000 -0.427 C -0.427 -0.692 0.000 C -0.427 0.692 0.000 C 0.000 -0.427 0.692 C 0.427 0.692 0.000 C 0.000 -0.427 -0.692 C 0.692 0.000 0.427 C 0.427 -0.692 0.000 C -0.692 0.000 -0.427 As for dodecahedra, that's just too large. I've upped the maximum number of faces to 147, and that takes care of it, but there are a few stray lines, since we are painting more triangles than actually needed. Just the way it goes, I guess Bob Dean Johnston wrote: Has anybody tried to create polyhedra with 12 or 20 vertices? The documentation seems to indicate that I should be able to go up to 20. I’m creating representations of shapes (Platonic solids, actually — maybe Jmol isn’t just for molecules anymore... :-). I would like to display an icosahedron and dodecahedron. I’ve created structures with a central atom surrounded by 12 or 20 atoms, but when I try and create the polyhedron, I get the following error message: Polyhedron error: maximum face(87) -- reduce RADIUS I have a feeling it’s creating more polyhedra faces than I want it to (I only want 20), but I’m not entirely familiar with how it works. I’ve gotten it to work just fine for tetrahedra and octahedra. Any insights, corrections, etc. are greatly appreciated. My testing page is at: http://www.otterbein.edu/home/fac/dnhjhns/jmoltest/poly.html Dean - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
