Re: [ccp4bb] ccp4-6.1.0: which ccp4.setup in Ubuntu Intrepid?

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: ccp4-6.1.0: which ccp4.setup in Ubuntu Intrepid?
From: Victor Alves vdalves {- at -} FMV {- dot -} UTL {- dot -} PT
Date: 2008-12-19

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Subject: Refmac and MSE?
From: Dima Klenchin klenchin {- at -} FACSTAFF {- dot -} WISC {- dot -} EDU
Date: 2008-12-19

Subject: Re: ccp4-6.1.0: which ccp4.setup in Ubuntu Intrepid?
From: "William G {- dot -} Scott" wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2008-12-19

When I "upgraded" to ibex it hosed my display, so this might not be of
much help, but in general,

1. You don't HAVE to use bash. You can use tcsh or zsh or any other
shell that suits your personal tastes. It just comes with a minimal
install to fit on a CD. Just issue

sudo apt-get install tcsh zsh

and you will have three shells to choose from.

2. To use tcsh, you can issue a command such as (after installing the
above),

chsh -s /bin/tcsh

(or even better, chsh -s /bin/zsh ).

3. You are right: setenv is indicates tcsh or csh

4. You can add directories to your path in any relevant startup
script or on the command line for that matter.

For all but tcsh and csh, use this syntax:

PATH=${PATH}:/your/new/directory ; export PATH

For tcsh and csh, use

setenv PATH ${PATH}:/your/new/directory

On Dec 19, 2008, at 6:01 PM, Victor Alves wrote:

>
> *
> *
> *
>
> Hi
>
>
>
> Doing my first installation of CCP4 and also a Linux newbie, so try
> to ?bear with me? ;-)
>
>
>
> The ?install.sh? CCP4 script created a ?setup-scripts? directory,
> with 2 shell subdirectories; ?csh? and ?sh?
>
>
>
> In ?/home/victor/.bashrc? I found 2 lines:
>
> source /usr/local/xtal/ccp4/setup-scripts/sh/ccp4.setup
>
> source /usr/local/xtal/ccp4/setup-scripts/sh/ccp4-others.setup
>
>
>
> So, I assume it is using the ccp4.setup-sh file.
>
>
>
> But Ubuntu Intrepid 8.10 uses ?bash?. If I type ?echo $SHELL?, it
> gives me /bin/bash, and Bash doesn?t use ?setenv? but ?export? (so I
> read).
>
>
>
> 1-Academic question: If I were to do a manual installation and
> chose, as a template for ?ccp4.setup?, the file?ccp4.setup-bash?
> (which uses ?setenv?) would I get into trouble?
>
>
>
> 2-If Ubuntu uses a ?bash? shell, why it is not using ?ccp4.setup-
> bash?
>
>
>
> 3-Which ?ccp4.setup? file is CCP4 using?:
>
> a) ?usr/local/xtal/ccp4/ccp4-6.1.0/include? or
>
> b) ?/usr/local/xtal/ccp4/setup-scripts/sh/ccp4.setup?
>
>
>
> 4-I manually installed CCP4MG and the instructions state to ?Add
> the CCP4mg "bin" directory to your PATH in ccp4.setup?, but the only
> place I found to do this was in ?/usr/local/xtal/ccp4/setup-scripts/
> sh/CCP4-OTHERS.SETUP? not ?ccp4.setup?.
>
>
>
> So I did:
>
> sudo gedit /usr/local/xtal/ccp4/setup-scripts/sh/ccp4-others.setup
>
> Added the following line, (right after a similar one for COOT):
>
> /usr/local/xtal/ccp4/ccp4mg-1.1.1/bin:
>
>
>
> After Login, I now have 2 lines for CCP4MG-1.1.1/BIN. What did I do
> wrong?
>
>
>
> echo $PATH (I reformatted one statement per line, for easier reading)
>
> /usr/local/xtal/ccp4/graphviz-2.20.2/bin:
>
> /usr/local/xtal/ccp4/fasta-35.4.1/bin:
>
> /usr/local/xtal/ccp4/clustalw-2.0.9/bin:
>
> /usr/local/xtal/ccp4/tcltk++/bin:
>
> /usr/local/xtal/ccp4/Python-2.4.5/bin:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0//bin:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/bin:
>
> /usr/local/xtal/ccp4/Coot-0.5/bin:
>
> /USR/LOCAL/XTAL/CCP4/CCP4MG-1.1.1/BIN:
>
> /USR/LOCAL/XTAL/CCP4/CCP4MG-1.1.1/BIN:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/share/dbccp4i/bin:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/ccp4i/bin:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/bin:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/etc:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/share/XIAROOT/xia2//binaries/
> linux_386:
>
> /usr/local/sbin:
>
> /usr/local/bin:
>
> /usr/sbin:
>
> /usr/bin:
>
> /sbin:
>
> /bin:
>
> /usr/games:
>
> /usr/local/xtal/chimera/bin:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/share/XIAROOT/xia2core//Test:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/share/XIAROOT/xia2core//Test/
> Compiled/linux_386:
>
> /usr/local/xtal/ccp4/ccp4-6.1.0/share/XIAROOT/xia2//Applications
>
>
>
> Thank you for your patience
>
>
>
> Victor Alves
>
> ______________________________
>
>
>
> VICTOR DIOGO ALVES, DVM PhD
>
> Professor Auxiliar
>
> Faculdade de Medicina Veterinaria
>
> UTL - Lisboa
>
> __________________________
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: ccp4-6.1.0: which ccp4.setup in Ubuntu Intrepid?
From: Victor Alves vdalves {- at -} FMV {- dot -} UTL {- dot -} PT
Date: 2008-12-19

Next message:
Subject: Refmac and MSE?
From: Dima Klenchin klenchin {- at -} FACSTAFF {- dot -} WISC {- dot -} EDU
Date: 2008-12-19