On Thursday 19 February 2004 19:34, mth wrote: > Rich wrote: > >> They need > >> to be moved independently into the unitcell in order to get the > >> correct effect. > > > > Well...not really, but.... > > > >> So, now I am puzzled. > >> > >> Q: When does *everything* get moved as a group?
Adding new unit cells to do unit cell box? > >> Q: When do things get moved to the group, but only on a > >> molecule-by-molecule basis? When you want to display one unit cell only and want to keep the sets (molecules) connected... > >> Q: Should this 'moving to the unitcell box' be automatic at load > >> time, or under user command? > > > > It is mathematically correct to take the atoms of the asymmetric unit > > (those that comprise the structure model) and apply all the symmetry > > elements of the space group. This generates a unit cell. > > OK, that makes sense. Ok, but that part is not covered yet... > > The problem is > > that to the person *viewing* this collection of atoms it may not be the > > view which best expresses the nature of the packing/interactions. At > > that point molecules associated with other unitcells are added to form > > the nicest picture. > > Yes, I understand how that would work. In my vision, Jmol scripts will take care of this in the end (in pseudo script commands) > show unitbox 3 3 3 > hide atoms 56 - 99 > show h bonds between atoms 5-9 > show h bonds between atoms 11-20 > set vanderwaals on > color atoms 77-5 # steric hindering > > The way this was often done for molecular entities was to generate all > > the molecules in the unit cell plus all those 1 unit cell to each side > > and then keep only those molecules with atoms inside the cell boundaries > > of the origin cell. At the expense of having more that the exact number > > of symmetry copies you got the complete view of the packing. I think this will be covered by the scripting commands... we will probably need some syntax for atom naming 76[0,0,0] to de note the 76th atom in a unit cell 0,0,0... BTW, Miguel, does the scripting language allow selecting of molecules, by first partioning into connectes sets, add (by Jmol) labels to those sets and then select them with a script command? Something like: > load samples/f1.cephalo > partition > select m1 > color red ? > OK. I can see that you would end up with 'extra' copies hanging off of all > of the edges. > You know that we hope to implement a 'multicell', so that would also help > a a bit. Indeed. Combine the multicell with scripting already available makes very much possible in making custom views... > > Some programs give you a finer level of control by allowing you to > > specify which symmetry operator plus translation is to be applied to the > > asymmetric unit. But this is usually only done to generate specific > > figures to illustrate particluar packing aspects. > > Not sure I understood all that ... but doesn't sound like a viable option. Right, again, I think scripting will take care of this... Once we have symmetry operations available too, we can apply these by scripting too... combine this with selecting one molecule from the unit cell ... > > For Jmol I'd probably pick the default action to be to display all > > molecules which have their (unweighted) centre of gravity within the > > unit cell. > > OK, that code works today (although it is *not* unweighted cg -- another > discussion topic) I think the unweighted) centre of gravity is simply the geometric center of the molecule, right? > Egon, your thoughts? Yes, and more will follow tomorrow... Egon ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
