On Saturday 30 August 2003 22:36, Peter Murray-Rust wrote: > At 17:09 30/08/2003 +0200, E.L. Willighagen (Egon) wrote: > >On Friday 29 August 2003 18:50, Miguel wrote: > > > >The Crystal class currently has no fields for its dimensions in terms of > > unit cells... I've planned to extend it for this purpose and will do this > > next week...The Iterator will take care of using this information in > > iterating over all Atoms that need to be displayed... And the Iterator > > will also take care of displaying the atoms in several ways: 1) the > > original atoms, 2) all atoms within the unit cell box. > > [I've discussed this with Egon...] > > Currently If a crystal cell is present Jmol translates all atoms to be > within the unit cell (by applying translations of the form +-l, +-m, +-n. > This makes no difference to the diffraction intensities but it does > reorganise the author's original atom position and may well destroy bonds. > when the crystal consists of discrete molecules I believe that most authors > create these as connected entities (sometimes called the crystallochemical > unit). It is not trivial to reconstruct these from the atoms within the > unit cell. indeed the authors may decide that certain atoms are bonded even > if they are further than normal covalent radii suggest. This is common > with transition metals such as copper. > > I would urge Jmol to honour the author's coordinates and preserve them for > display rather than unnecessarily destroying some of the information. It is > easy to translate atoms into the unit cell if this is really required > (though there are few cases where I personally would find this valuable).
The original coordinates are taken as is... in the crystal dialog in the extra menu you can select 'original' coordinates... It becomes a bit more problematic, though, when symmetry operations are taken into account... then the bonded molecules (crystallochemical unit) may be placed well outside the displayed unit cell... But that can be solved too... Egon ------------------------------------------------------- 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
