Egon, Thanks for the discussion this morning ... it was very enlightening for me.
Two items we need to discuss. 1. connected sets I now understand that I need to determine connected sets prior to shifting to the unit cell. This means that, in cases where the file does not contain bonding information, I need to apply the auto-bonding prior to doing the shift. However, shelx files are in fractional coordinates. That means that I have an extra step with these. - if the input data is in fractional coordinates then conver to euclidean space After that, it will run the same as usual - if there is no bonding information then auto-bond - if it is a crystal, then putAtomsInsideTheUnitcell - if weMovedAnyAtomsInsideTheUnitcell then rebond Where putAtomsInsideUnitcell will use the connectivity data to determine how to do the shifts. Please confirm that this looks right to you. 2. IxJxK crystal matrix I think this is a good task and I am glad that you are interested in working on it. However, I do not think it is simple and I think we need to work on it together ... at least to get started. I believe that it will take several weeks to implement this. But the end result will be good. Some of the architectural issues we will face will directly apply to animations and vibrations, so it will have good payoff. I think that there are some significant issues involved. Some of them are 'crystalography' in nature ... like bonding between the cells. Others are implementation dependent ... like the way that the graphics engine works. First, we need to *really* think about whether we want to try to duplicate the atoms, or whether we want to try to handle everything by translating the one unitcell to new positions. Let's start this discussion and we will go from there. Miguel ------------------------------------------------------- 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-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
