Dear List, I'm running the Jmol application, 11.8.4, on Mac OS X 10.5.8.
I'm having trouble invoking Jmol via command line options as indicated in the Jmol wiki page for the application (http://wiki.jmol.org/index.php?title=Jmol_Application) For example, if I use: $Jmol -ionx myscript.spt molecule.pdb and mysrcript.spt is: select all; write coords pdb one.pdb; select none; then one.pdb is created, but it is empty. Similarly, if myscript.spt is: #set atom variables ONE="[ACE]1.O" TWO="[AIB]4.N" #clear previous measurements measurements delete #make measurement: measure all ({...@one}) ({...@two}) #Place measurement in variable dist dist=script("show measurements") name="dist" + ONE[6] + TWO[6] + ".txt" #write file for importing into Igor write VAR dist @name dist="" then, dist14.txt is created, but is empty except for "Show measurements." I suspect that Jmol is not loading the pdb file specified in the command $Jmol -ionx myscript.spt molecule.pdb What am I doing wrong? Do these command line options work on the Mac? (These scripts work as expected when invoked from the console in an open version of Jmol.) Matt PS Using $ jmol -s myscript.spt molecule.pdb provides the requested results, but it leaves Jmol open. ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
