----- Original Message ----- From: Jan Reichert <[EMAIL PROTECTED]> Date: Thursday, February 5, 2004 12:53 pm Subject: [Jmol-users] 2x1 asymmetric units
> >For example, many soil-forming clay minerals have isomorphous > substitution...essentially replacement of one element for another, > such as Al3+ or Fe3+ for Si4+ in tetrahedral sheets and Mg2+ or > Fe3+ for Al3+ in octahedral sheets. Either we'd define a very > large quasi-unit cell that would have all these substitutions in > place (which we currently do in a _large_ pdb file) or load the > basic structure and then script redefinition of the element name > and charge based on how many unit cells are involved. > > > > > but, in this case, using one large PDB file is appropriate. Not certain in what sense 'appropriate'. There is no fixed position for these substitutions. I'd like to be able to generate 50 cells with 100 Al sites, and then randomly replace 10% of them with Fe and another 10% with Mg (to follow the formula below). For other variations of the same mineral, the proportions of substitution would be different, of course. Just to clarify the thrust of this point: I'd like to have all the atoms generated by replicating a unit cell _numbered_ so that they can be manipulated by scripts. > > >For interest's sake, one clay mineral of interest has a formula: > >(Al_1.6 Fe_0.2 Mg_0.2)(Si_3.9 Al_0.1)O_10 (OH)_2 [smectite] > >Those substitutions are important for the cation exchange and > water sorption properties of the material and so must show up in > order to make the model of value. Of course, many more minerals > than just this have 'random' substitutions that are part of the > story we want to tell. > > > >--Phillip Barak > >Dept of Soil Science > >Univ of Wisconsin-Madison ------------------------------------------------------- The SF.Net email is sponsored by EclipseCon 2004 Premiere Conference on Open Tools Development and Integration See the breadth of Eclipse activity. February 3-5 in Anaheim, CA. http://www.eclipsecon.org/osdn _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
