On Saturday 04 October 2003 19:30, Miguel wrote: > > On Friday 03 October 2003 23:13, Miguel wrote: > >> > A second thing is, that we need to be able to display more than one > >> > >> unit cell, but say 2x2x2 unit cells... with all content... Again, > >> this is were the iterators come in... here the iterator repeats the > >> process in the previous paragraph for each unit cell it has to > >> plot... > >> > >> So, this is new functionality ... Correct? > > > > Well, it was in Jmol b6, but at least new to the CDK based Jmol.. > > So, you are saying that this functionality exists in b6?
Yes, b6 can show just one unit cell, but using the crystal box in the extra menu, you can also display a 100x100x100 (never actually tried that...) > What are the steps I need to go throughto see it in b6? We need a mechanism to store the crystal dimensions A,B,C (A := number of unit cells in the a axis direction, etc) in Crystal.java in CDK, I'll do this... Secondly, we need the CrystalIterator display the atoms in all these unit cells... > >> If so, then educate me a little more on this. Is it the case that you > >> want the same atom structure repeated, but with a base at a different > >> offset? > > > > Correct. > > OK. > Then it seems to me that there is a better way to handle this. > All one needs to do is repeat the same atoms, but translated to different > positions in 3-space. Yes, that was the proposal I was trying to make... only the symmetry unrelated atoms are stored in Crystal... Both unrelated to translation symmetry, *and* within cell, symmetry operations due to the spacegroup... > Are these offsets the corners of the unit cell box? If not, how does one > calculate the offsets of the neighboring cells? Yes. > It seems to me that we can render this to the screen without duplicating > the data strutures. Absolutely! Sorry for not making my expanations clear enough ;) > That is, I can render the same set of atoms, with all > of the atoms offset by specific amounts. That will be much simpler, will > take up much less memory, and be just as fast. > > Also, you can expand it to as many levels as you want ... we do not have > to restrict it to 2x2x2. Well, it's nice to see that we have the same thought about it... > Finally, this should have a benefit in scripting. Any visual changes > (color, size, hiding, etc) that are made to the atoms of the "true" cell > will automatically be replicated to all the other "phantom" cells. > > Fabian & Egon ... does this sound right? ;) Couldn't be more right... Egon -- PhD Molecular Representation in Chemometrics Laboratory of Analytical Chemistry http://www-cac.sci.kun.nl/people/egonw.html ------------------------------------------------------- This sf.net email is sponsored by:ThinkGeek Welcome to geek heaven. http://thinkgeek.com/sf _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
