On Thursday 05 February 2004 19:48, Miguel Howard wrote: > We had some of this discussion a few months ago. Bits and pieces are > coming back to me. > > The other disadvantage of 'replicating' the unitcell is that there will be > no bonding between cells. > > Q: Is there a solution to this problem?
Ok, because you cannot apply the rebonding...? Possibility one: molecular crystals Those are crystals of molecules, small or even proteins. At least in small molecule crystals it is common to define the atoms in a complete molecule, with bonding, even if this molecule crosses the edge of a unit cell. In this case, it should be no problem. *Unless* the program 'folds' atoms back into the central unit cell... This is currently the default behaviour in Jmol b6. Possibility two: metallic crystals/zeolites/salt crystals etc In this case, there are no distinct molecules, and the whole of the crystal is connected by bonds, with covalent bonds (e.g. zeolites), or ionic bonds (e.g. salts), or metal bonds (metals ;)... This is mostly the working field of Fabian, and in this case every thing is bonded. For these crystals, atoms are only showed within the unit cell, because there is not such thing as 'keeping the molecule in one piece'. Jmol b6 has the option to independently define a crystal box for bonds and for atoms. That said, I get to your question again. I'm not that familiar with the algorithm Jmol HEAD uses to draw a scene... but I could imagine this pseudo code: 1. given crystal box for bonds and atoms (those might be identical), take the largest one 2. for each atom in the atom crystal box draw it 3. for each bond in the bond crystal box draw it Meaning: why can't a bond be drawn if the two connected atoms are not drawn? Why is this situation different from say "Vanderwaals radius == 0"? So I'm trying to say: replicate as so that the max(bond crystal box, atom crystal box) is filled, and then start drawing atoms and bonds, and draw only if bond within bond crystal box, and draw only atom if in atom crystal box... Am I a bit clear on what I'm trying to say?? > Q: Within the file formats, is there a way to specify the bonding that > exists between cells? In CML that would be possible... In possibility one, there is not other bonding between cells, than the covalent bond within the molecule + possible hydrogen bonds + ionic interactions. For possibility two, all is connected if within covalent radius. Unit cells itself are not really bonded... Egon ------------------------------------------------------- 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
