Hi Stephano, I don't see the directory /Applications/Ifeffit/bin on your search path. It should be there. It is usually automatically included via a script installed by the Ifeffit installer, but it seems to be missing here (perhaps another installer deleted it by mistake). Add the following line to your .cshrc file in your home directory and see if it fixes things. Be careful to use a text editor that understands unix line endings (like the free editor smultron from http:// smultron.sourceforge.net). source /Applications/Ifeffit/bin/iff_init.csh Paul On Sep 19, 2006, at 6:00 PM, Stefano Ciurli wrote:
Hi Paul,
Looking over your comments, I must admit I am a little confused as to what could be causing the problem. If you can invoke aquaterm complete with functioning graphics, the only difference that I can guess could exist is a difference in shell paths. The runprog program with its attendant shell variable changes seems to work fine. The AppleScript program is pretty minimalist, so the only viable explanation I can think of is somehow the shell environment getting corrupted. As the AppleScript that invokes artemis works fine here (and apparently elsewhere as well), a possible cause is the difference in startup initialization at the shell script level.
if you need my .cshrc file, here it is below, maybe you can guess if something is wrong:
bindkey -k up history-search-backward bindkey -k down history-search-forward if (! $?DISPLAY) then setenv DISPLAY :0.0 endif source ~/Library/Scripts/iterminal_custom.tcsh source /Applications/XtalView/XtalView.env source /sw/bin/init.csh setenv PATH `echo $PATH`:/Applications/Sparky.app/Contents/ Resources/bin:/usr/local/sparky/bin:/usr/local:/usr/local/ molscript:/usr/local/bin:/Applications/XtalView/bin/powermacDarwin:/ Applications/vnmrj1.1d/bin:/Applications/cyana-2.1:/Applications/ cara_1.2_osx:/Users/stefano/AutoAssign2.3.0:/Users/stefano/bin defaults write com.apple.x11 wm_ffm true defaults write com.apple.x11 no_quit_alert true setenv PGPLOT_DIR /etc setenv PGPLOT_DEV /AQT setenv SPARKYHOME /Users/stefano/Programs/Sparky setenv EDENHOME /usr/local/eden setenv ODAT /Users/stefano/Programs/o/data setenv MARSHOME /Applications/mars-1.1.3_OSX setenv CCPNMR_TOP_DIR /usr/local/ccpnmr setenv PYTHONPATH .:$CCPNMR_TOP_DIR/ccpnmr1.0/python setenv LD_LIBRARY_PATH /sw/lib:/sw/lib:/usr/X11R6/lib setenv LD_LIBRARY_PATH ${CCPNMR_TOP_DIR}/tcl8.3/lib:$ {CCPNMR_TOP_DIR}/tk8.3/lib setenv TCL_LIBRARY /sw/lib/tcl8.4 setenv TK_LIBRARY /sw/lib/tk8.4 alias runmars $MARSHOME/bin/runmars alias ono osx_ono alias cara /Applications/cara_1.5.2_osx
if (-e /Applications/NMRPipe/com/nmrInit.mac.com) then source /Applications/NMRPipe/com/nmrInit.mac.com endif if (-e /Applications/NMRPipe/dynamo/com/dynInit.com) then source /Applications/NMRPipe/dynamo/com/dynInit.com endif # this line was added by Ifeffit Installation Script source /Applications/Ifeffit/bin/iff_init.csh ~
Bruce, Matt, what do you think about this? If a shell is started by AppleScript, it would be a non-interactive shell, whereas if it is started manually via X11 and the default shell is bash, the startup initialization file ~/.bashrc would be read in.
my default shell is tcsh
If it were invoked via the AppleScript program, it would not. Sounds like something is screwy with the PATH environment variable. Of course, this implies that it is something unique to Stefano's system and not general (never mind the fact that the user can switch shells -- I am using bash on one system and tcsh on another!).
let me know which configuration file I should look at
If a path was set incorrectly (e.g. affecting a perl library or otherwise), could this cause the symptoms that Stefano is seeing? I might add that I notice the default path for feff6 is "feff6" so this would seem to implicitly assume that feff6 is on the users path (and it obviously isn't in this case, although it is for me). One fix would be to hardwire all of the paths needed into the runprog shells script by appending to the PATH variable (e.g. the location of artemis is wired). Any suggestions?
will see what Matt and Bruce have to say Stefano -- ____________________________________________
Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203
"Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI
"Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high" _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit