[Ifeffit] Artemis error message and paths

Paul Fons paul-fons at aist.go.jp
Tue Sep 19 21:04:55 CDT 2006

   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:// 

   source /Applications/Ifeffit/bin/iff_init.csh

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 at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20060920/1fc8e4c9/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: smime.p7s
Type: application/pkcs7-signature
Size: 2423 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20060920/1fc8e4c9/attachment.p7s>

More information about the Ifeffit mailing list