[Ifeffit] Artemis error message and paths

Stefano Ciurli stefano.ciurli at unibo.it
Tue Sep 19 04:00:19 CDT 2006


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"
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