Hi Martin,
I have modified the cns.sh file by removing the _SW_PREFIX_ with /sw , for your
information I've copied the contents of this file to the email, just in case it
contains any other surprises! I've also looked in my .cshrc file in my home
dir and don't see any "." in any of the path's. I've also copied this to the
email for diagnosis. I'm sorry in advance if the file looks badly written, but
it works for all of the crystallography programs that I use. ( If you have any
suggestions as to how to make it more efficient I would be very grateful! )
I tried the command type - a cp and get the error message "tcsh: type: Command
not found." in the c-shell, although the command works in the bash shell and
outputs "cp is /bin/cp" which looks normal. Should I reinstall the cp
program, and if so how would I do this? I also looked in /usr/local/bin/cp and
/sw/bin/cp and see no other version of cp. Can I change the -d flag in the
install script to something else, or would that be a bad idea?
best,
Simon.
.cshrc file
[bio-sln1:~] simonn% more .cshrc
test -r /sw/bin/init.csh && source /sw/bin/init.csh
source /usr/local/ccp4-5.0.2/bin/ccp4.setup-csh
set path = ( $path /usf/dejavu /usf/rave /usf/xutil /usf/molscript-2.1.2 )
set path = ( /usr/local/arpwarp/arp_warp_6.1.1/bin/`uname` $path )
setenv warpbin /usr/local/arpwarp/arp_warp_6.1.1/bin/`uname`
set path = ( /usr/local/phaser $path )
alias ono /usf/ono/bin/osx_ono
alias topdraw /usf/dundee/topdraw
alias mtz2sca /usf/mtz2sca/mtz2sca
alias whatcheck /usf/whatcheck/whatcheck_Panther_binary
alias draw /usf/bobscript/draw
alias bobscript /usf/bobscript/bin/bobscript-macosx
alias coot /usr/local/coot_sw/bin/coot
alias mosflm_sd /usr/local/mosflm_sd/mosflm_macOSX_SD
setenv ODAT /usf/ono/data
Modifies cns.sh file; originally the file contained SWPREFIX=_SW_PREFIX_
[bio-sln1:/sw/etc/profile.d] simonn% more cns.sh
# Initialize CNS for bash and zsh
SWPREFIX=/sw
export CNS_SOLVE=$SWPREFIX/share/xtal/cns_solve_1.1
export CNS_LIB=$CNS_SOLVE/libraries
export CNS_MODULE=$CNS_SOLVE/modules
export CNS_TOPPAR=$CNS_LIB/toppar
export CNS_CONFDB=$CNS_LIB/confdb
export CNS_XTALLIB=$CNS_LIB/xtal
export CNS_NMRLIB=$CNS_LIB/nmr
export CNS_XRAYLIB=$CNS_LIB/xray
export CNS_XTALMODULE=$CNS_MODULE/xtal
export CNS_NMRMODULE=$CNS_MODULE/nmr
export CNS_HELPLIB=$CNS_SOLVE/helplib
CNS_UTILS_PATH=$( dirname $(/bin/ls $CNS_SOLVE/*/utils/plot_patterson |
head -1) )
export CNS_UTILS_PATH
PATH=$CNS_SOLVE/bin:$CNS_UTILS_PATH:$PATH
export PATH
[bio-sln1:/sw/etc/profile.d] simonn%
On 2 Jun 2005, at 09:41, Martin Costabel wrote:
Simon Newstead wrote:
Dear Martin,
Thanks for the information. I just have a few questions regarding your
suggestions.
1. Move /sw/etc/profile.d/cns.sh out of the way or repair it,
How do I do this? I see that this script is only for setting the variables for
the CNS program to run in either the bash or ksh terminals. do I just rename
this, or do I need to move it out of the profile.d directory?
It seems to crash, though. The error message looks as if your version of cns.sh
contains the string"_SW_PREFIX_" where it should contain "/sw".
Either edit it with a text editor, like
sudo vi /sw/etc/profile.d/cns.sh
and replace _SW_PREFIX_ by /sw, or move it out of the way, i.e.
sudo mv /sw/etc/profile.d/cns.sh ~/cns.sh_saved
2. remove "." from your PATH,
Again, not sure how I do this? Where do i find my PATH? I usually just edit my
.cshrc file in my home directory.
Yes, that's the place where PATH is set. You must have some line in your
~/.cshrc where "." gets put in front of PATH. Remove this line or make sure
that "." is placed at the end of PATH, not at the beginning.
3. move your unusual "cp" binary out of the way
I am not so sure about this one; look at the output of "type -a cp" and if there
is a /usr/local/bin/cp or /sw/bin/cp, try to rename them temporarily and see if
this changes anything.
[]
This confuses me too, although probably for totally different reasons! I never
get the error messages that you speak of, and the CNS program runs fine.
I have no explanation for this, except perhaps some strange setting of
environment variables that avoid from the command line the error that fink
sees. But it would first be interesting to see what is actually the contents of
your cns.sh. Maybe it's something more complicated than I can imagine.
--
Martin
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