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Subject:

Re: environ.def / default.def

From:

Eike Schulz <[log in to unmask]>

Reply-To:

[log in to unmask]

Date:

Sat, 17 May 2008 18:45:31 +0200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (246 lines)

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/
> 

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