Sorry -- I think I forgot to upload the latest changes. Please try again. Bob
Frieda Reichsman wrote: > Hi Bob, > > Trying out the new commands on > http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm > > and I am getting errors such as > > script compiler ERROR: command expected > ---- > >>>> file 0 <<<< > > and > > script ERROR: java.io.FileNotFoundException: > http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/data/cholesterol.mol > ---- > load >> "cholesterol.mol" << > > Frieda > > > > > On Feb 14, 2007, at 7:01 PM, Bob Hanson 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 >> <http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> <mailto:Jmol-users@lists.sourceforge.net> >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > /////////////////////////////////////////// > > > Frieda Reichsman, PhD > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /////////////////////////////////////////// > > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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 >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. 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