in most cases I only want to see two asymmetric units , but there I would like to address every residue, especially at the interface between them.----- Original Message ----- From: "E.L. Willighagen" <[EMAIL PROTECTED]>
I wonder what is the right way to represent these extracells/atoms in
memory.No, it would be much better to only store the atoms on the central unit cell... the atoms in other unit cells are only drawn not stored...
I'm ok with writing out the need for spacegroups at this time, but I think that I'd like to see all the atoms generated from the unit cell given names, numbers, labels, etc. so that they are manipulatable by scripts.
Using the select within would be especially helpful.
select within(4.2, *{x,y,z}) and *{.5-x,-y,.5+z}
if we use '{}' to address the subunits in scripts?
Regards, JanFor 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.
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
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