Egon wrote: > 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
One of the ways we want to extend the crystal functionality of Jmol is by creating a multicell crystal of the user's dimensions. So we can look at a unitcell or create an IxJxK multicell (... and it is going to be 'wicked' :-) Once we do this, we will need a way to uniquely address each of these unitcell copies. That will allow us to use the scripting language commands to change the rendering of individual atoms/bonds within the multicell in order to hilite special features. I trust that there is a standard nomenclature/addressing scheme that is used in the crystallography world. Q: Unitcells are probably addressed by their fractional coordinates [0,1,-1], correct? Q: I don't want to go into too much detail on this yet, but can someone tell me what the general scheme is for naming one of these reflection / rotate / spacegroup copies that is within the unit cell ? There are two pretty important places that we need to squeeze this in. 1. the data structures 2. the scripting language Now, Jmol already has some support for holding more than 1 copy of the same thing. PDB files have the concept of a 'model' that is supposed to be multiple copies of what is fundamentally the same thing. And, because of the PdbModel, the scripting language already has support for addressing each of these models individually. I would like to explore the idea of trying to reuse some of this infrastructure to support two different things ... PdbModels AND multicells The obstacle that would prevent this reuse would be the presence of PDB files that contain both CRYST1 and MODEL records. It looks like to me that the PDB spec will not allow multiple models, each of which has its own CRYST1 records (!Gracias a Dios!). However, the spec looks like it would allow multiple models, all of which fit within the same CRYST1 unitcell. Q: Does someone know the answer to this? (Uhhh ... Rich?) Q: Any other comments/observations? Thanks, 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-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
