> Miguel wrote: > >>One way that I thought of handling it was to take a unit cell and grow it >>into a crystal by creating a new model on the fly. I think that we could >>handle that. >> > Ah, that be a nice solution that doesn't require any symmetry-handling > (only symmetry-delivering) at file load time. This could add up to a > large, messy number of frames, though, as the user tries different unit > cell options.
I don't know. I had not considered that there could be a large number of frames. I figured that someone would create a half dozen different crystal sizes and that would be enough. > (Or could one delete whole models/frames as well?) I had not considered deleting whole models/frames. I would certainly be a much more tractable problem than deleting individual atoms. The most obvious problem is that the atoms are identified by atom index. There are implicit references to these atom indexes in the BitSet instances. In addition, we may expose these atom indexes to clients through the Java+JavaScript API. So, if we every have to reorganize/compress the atom index 'address space' then we are going to have problems. I think that we should avoid deleting models/atoms if at all possible. > It has > the advantage that the crystal would "sprout" from the unit cell without > changing the centering. That would certainly be nice. > > But, then again, if you already have a set of frames that are > independent models, then the new frames will certainly end up being a > hodge-podge of models. > Hmm, I don't know.... I might vote for keeping it very simple -- the > file is loaded with a set number of cells defined. So, is it the case that you are thinking that you would set some "crystal" variable and then load the file? >>I did not understand much of this. Please try to clarify for me. >> > One will want to, say, click on an atom and select THAT set of bonded > atoms -- THAT molecule. There should be some way of selecting "all atoms > in this molecule" like there is "all atoms in this chain" for proteins > and nucleic acids. Imagine > > set picking MOLECULE Got it. That makes sense. Raises another question ... Q: Is it the case that the unit cell always contains a single molecule? Or can the unit cell be made up of more than one molecule? It seems to me that I have seen unit cells with more than one molecule, but maybe the molecules were duplicated in order to get to a simpler space group. Miguel ------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid0709&bid&3057&dat1642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
