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/ >
