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Re: [ccp4bb] environ.def / default.def |
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CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 17 May 2008Subject: Re: environ.def / default.def From: Eike Schulz eschulz1 {- at -} GWDG {- dot -} DE Date: 2008-05-17 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/ CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 17 May 2008 |
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