Dear Eike:
I think I was still asleep when I sent that last email. I am very
sorry for writing "Eric". Maybe I need to get glasses.
tcsh and zsh are both much more user-friendly than bash, and most
crystallography programs seem to assume the user is using tcsh, so
that might be the best choice.
However, if you really want to geek out, zsh is a lot of fun.
Bill
On May 17, 2008, at 9:45 AM, Eike Schulz wrote:
Hello Bill,
thanks a lot for making such big effort.
It is a real pity but the syntax does not work properly. However, I am
more or less convinced now that the whole thing is a bash / (t)csh
related problem. It might be the easiest way just to switch to a
different sh flavour as login shell. I hope that will settle the
issue.
Regardless of the success I learned a lot thanks to you and many
others.
The link you provided seems to be a good compilation of necessary unix
knowledge - I will try to circulate it among my colleagues.
Thanks again and all the best.
Eike
On Sat, 2008-05-17 at 08:13 -0700, William Scott wrote:
Hi Eric:
You shouldn't have to source or do anything with the def files.
There seems to be some problems with the ccp4.setup-bash from what I
have seen. If it gets sourced more than once, spaces get introduced
into the PATH variable, which creates havoc. The file also locally
defines "setenv" to try to use the csh syntax, which may or may not
be
problematic.
I've made one that should avoid these problems and I tried to set it
up to what looks like you need for your system. So, please try the
following:
1. Eliminate all the directives to source any setup and def files
from your shell startup dot files.
2. Put this file somewhere and source it.
HTH,
Bill
PS: The zsh and tcsh shells are both more user-friendly than bash,
so
you might find those easier (what I sent you should work with zsh,
although I have a much better one that makes use of zsh customizable
completions and so forth).
Here's some more info on unix shells: http://xanana.ucsc.edu/xtal/unix.html
On May 17, 2008, at 1:48 AM, Eike Schulz wrote:
Hello again,
sourcing environ.def or ccp4.setup-bash did not help to make it
work.
Sourcing default.def results in
--------------------------------------------------------------
bash: memory: command not found
bash: !FITING_NR=500000: command not found
bash: !TRAING_NR=500000: command not found
bash: !ROTING_MI=600000: command not found
bash: !ROTING_MC=2900000: command not found
bash: !TABLING_MI=1500000: command not found
bash: !TABLING_MR=5400000: command not found
---------------------------------------------------------------
debugging info:
---------------------------------------------------------------
echo $CCP4
/usr/local/software/ccp4/ccp4-6.0.2
echo $CCP4I_TOP
/usr/local/software/ccp4/ccp4-6.0.2/ccp4i
echo $PATH
/usr/local/software/ccp4/ccp4-6.0.2/src/phaser/phaser-2.1.1/build/
intel-linux/bin
/usr/local/software/ccp4/ccp4-6.0.2/ccp4i/bin
/usr/local/software/ccp4/ccp4-6.0.2/etc
/home/eschulz1/bin
/usr/local/bin
/usr/bin:/bin
/usr/bin/X11
/usr/X11R6/bin
/opt/kde3/bin
/usr/lib/jvm/jre/bin
/usr/lib/mit/bin
/usr/lib/mit/sbin
/usr/local/software/XDS-linux_ifc_Intel+AMD
/usr/local/software/coot-Linux-i386-redhat-8.0/bin
/usr/local/software/ccp4/ccp4-6.0.2/bin
/usr/local/software/ccp4/ccp4-6.0.2/include
--------------------------------------------------------------
I hope this helps you ...
Thanks again an best regards
Eike
On Fri, 2008-05-16 at 20:37 -0700, William Scott wrote:
Probably. You should source either the first or the second file
depending
on your shell (the first for bash, the second for tcsh/csh). That
might
be the cause of your subsequent problem.
For purposes of debugging, can you send us output for the following
three
commands:
echo $PATH
echo $CCP4
echo $CCP4I_TOP
On Fri, May 16, 2008 5:22 pm, Eike Schulz wrote:
Hello again,
thanks to some people for their fast and helpfully very detailed
advice:
Including
________________________________________________________________
source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash
source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup
________________________________________________________________
into my .bashrc did indeed solve the problem with MTZDUMP when
executed
from the shell. Further thanks for some other corrections. But
unfortunately the error persists when I try to run refmac from the
ccp4i
GUI - it complains not to be able to extract data from an .mtz
file.
Did I miss anything important?
Kind regards
Eike
On Fri, 2008-05-16 at 14:37 -0700, William Scott wrote:
On Fri, May 16, 2008 1:06 pm, Eike Schulz wrote:
Hello everybody,
----------------------------------------------------------------
setenv CCP4_MASTER /usr/local/software/ccp4
setenv CCP4 $CCP4_MASTER/ccp4-6.0.2
For bash, zsh, etc, you need to start with
export CCP4_MASTER=/usr/local/software/ccp4
export CCP4=$CCP4_MASTER/ccp4-6.0.2
setenv is specific to (t)csh.
export is specific to the sh-like shells.
---------------------------------------------------------------
... and the .bashrc contains following entries:
---------------------------------------------------------------
PATH="$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/"
PATH="$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/"
/usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-bash
---------------------------------------------------------------
I think that last line would need to be
source /usr/local/software/ccp4/ccp4-6.0.2/include/ccp4.setup-
bash
and you shouldn't need this line:
PATH="$PATH:/usr/local/software/ccp4/ccp4-6.0.2/include/"
and you should get rid of the trailing slash on this line:
PATH="$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin/"
to make it
PATH="$PATH:/usr/local/software/ccp4/ccp4-6.0.2/bin"
but if ccp4.setup-bash works, you shouldn't need to explicitly
set any
PATH, including the one you missed (for ccp4i).
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
