From: Bob H. <bob...@gm...> - 2007-04-14 03:59:07
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Christian, There really should be no need for two models. If you have the capability to build the models with an overabundance of atoms, that's even better. Just use that larger model. use clipping planes or even just select within (0.5, cell=555) to fine tune the atoms you want, then you will see the open tubes. It's only if you include isosurface..... ignore (xxxx) that you will see the closed ends then. On 4/13/07, Christian Baerlocher <bae...@ma...> wrote: > Hi Bob, > > Thanks for your help. I think I understand now how it works. It is > indeed tricky, but I think I can get it to work. > > However, I still have a few problems: > > I cannot use the cell selection, as this is too crude. I need to > specify fractions of cells, i.e. I may need boundaries such as {-0.2 > 1.2 -0.3 1.3 0 1.0} in order to get nice tubes. So I have > written a small program that gives me two models, one with all atoms > within the desired range and one with only atoms outside this > boundary. By selecting only the "inside" atoms of the first model I > get the desired open tubes. This works, but maybe there is a cleverer > way to do this. The openings are a bit jagged, but I think this > cannot be changed. the jaggedness will be there, but you can make it a bit smoother by changing the isosurface resolution. > > So far so good. Now the problem: in order to get the channel system, > we fill it with spheres that have different radii. I want now to > calculate the surface around these "atoms", so I need to specify > their radii in Jmol. I tried it with spacefill, which works fine for > the atom display, but these are not used in the calculation of the > isosurface. I need to define the VDW radii myself, but I did not find > a way to do this. Is there one? No, but that would be a fine use of the DATA statement. Consider using isosurface cavity It won't be open, but it will be the exact surface around your "atoms". This algorithm inserts the exactly fitting sphere for a cavity at each 3D grid point. The result is a set of overlapping spheres of the radii you describe. Then the surface is drawn around those spheres. Should be perfect. I think I could write something that would open it up on the outsides if that is the only thing you need to make isosurface cavity do what you need. By the way, the voxel count in that cavity gives you a measure of its volume pretty closely, I suspect. > > Of course, I will be glad to send you the result of my efforts. So > far I have only an experimental page which is not yet properly > connected to the zeolite database and which shows no channel surface > yet. :-) > look at > http://crystals.ethz.ch/IZA-SC/3D-images/JmolViewer.php? > cifname=LTA&FTC=LTA&acell=%2011.919&bcell=%2011.919&ccell=% > 2011.919&alpha=%2090.000&beta=%2090.000&gamma=%2090.000 > > to see just one example of a zeolite (all on one line) > lovely. > Cheers > > Christian > > > > > Date: Tue, 10 Apr 2007 10:28:40 -0500 > > From: "Bob Hanson" <bob...@gm...> > > Subject: Re: [Jmol-users] slab/depth in more than one direction > > To: jmo...@li... > > Message-ID: > > <ac1...@ma...> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Hmm, this is tricky, and the solution may not be practical. > > > > 1) The internal arbitrary-plane slabbing is specifically for atoms, > > not surfaces. So you can select atoms this way, but you cannot cut > > surfaces with it. > > > > 2) All you need is a few more atoms. Instead of building a single > > unitcell, make 27 using > > > > load xxx.cif {444 666 1} > > > > Now you only DISPLAY the center cell: > > > > display cell=555 > > > > but all the other atoms are there, so when you do > > > > select displayed > > isosurface sasurface > > > > you will get the isosurface for the atoms you see, and you will get > > those open ends you are talking about. (Please show me -- I love > > zeolite structures.) > > > > Also, I would recommend trying > > > > isosurface sasurface 0 > > > > not just "sasurface". The default there is whatever is set as the > > current solventProbeRadius, which has a default of 1.2 Angstroms. I > > would think (maybe) what you want for your display is 0, which gives > > the van der Waals radius surface instead. Maybe? > > > > Also, have you checed out > > > > isosurface hkl {h k l} map sasurface > > > > ? This is a very cool-looking plot. > > > > > > Bob Hanson > > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |