I have just checked in a version of Jmol that allows: inverting selected atoms about points and planes
writing of selected coordinates and orientation reading those files back into Jmol Basically, there is a new command: invertSelection which by itself inverts all atoms through the center of rotation invertSelection POINT [some point description] which inverts selected atoms through a point invertSelection PLANE [some plane description] which inverts selected atoms across a plane Now, once this is done, of course, the atoms are not where they used to be. That would mess up the state, so I have added a new DATA type called "coord": DATA "coord set" 24 ; Jmol Coordinate Data Format 1 -- Jmol 11.1.13 2007-02-14 15:54; 1 H H1_#1 2.9400268 2.3187106 -0.35901633 ; 2 N N2_#2 -1.4280989 2.2970076 0.9680812 ; 3 C C3_#3 -0.5195322 0.37288004 -0.24890617 ; ... 24 H H24_#24 0.7507625 -1.5374694 -1.5575587 ; end "coord set"; which allows setting of atom coordinates in bulk. This is necessary, of course, because if you move the atoms, we have to reproduce that in the script. So with that, it seemed simple enough (about 10 lines of code) to create: write coords which writes the same SPT script as write state except it also includes coordinate positions. SO, having done that, it seemed ridiculous if Jmol could write coordinates but not read what it had written, so I added a tiny JmolDataReader to read those files. I really don't know if that is of any particular use. But it was simple enough to do. But more useful, probably, would be the ability to write the coordinates in a more standard format, and if people feel strongly that we should NOT be able to read these script files this way, I would be happy to remove that capability. Comments? Suggestions for perhaps a SIMPLE general format for writing coordinates? XYZ? (no number limitation, but no bonds), MOL? (limited, but with bonds), PDB? (unlimited, but rather involved). Alternatively, should Jmol have a new "native format" that includes the "state"? I don't want to make a big deal about this; just wondering. And, yes, I know -- the next thing needed is "rotateSelected". I'm working on that. When that is in, we can start having quite some fun with loading two files, inverting one, moving it above the other, rotating it independently, etc. I think there might be some nice applications that would use this capability. Bob ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
