> I have just checked in a version of Jmol that allows: > inverting selected atoms about points and planes I like it! I thought about asking to add something like this a while back, but never got around to submitting an official feature request. I can think of some really nice ways of using this capability. (I'm working on some pages that illustrate concepts of point-group symmetry - see http://www.otterbein.edu/home/fac/dnhjhns/xmltest/demo.html ) I still haven't had time to digest the cool new scripting capabilities...
> And, yes, I know -- the next thing needed is "rotateSelected". I'm > working on that. Any chance you can think about improper rotations as well? :-) > 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"? If Jmol is creating it, what you have looks ok (except for connectivity). I don't know if bonds should be stored like MOL files or as Jmol commands (like the state). I like the idea (in principle) of using XML, though it certainly doesn't fit the "simple" criterion. Dean On 2/14/07 7:01 PM, "Bob Hanson" <[EMAIL PROTECTED]> wrote: > 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 ------------------------------------------------------------------------- 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
