Thanks, Francois! 

To define a permanent variable and source it in bashrc. That's really a good idea. 
But Ralf's suggestion seems more amazing, why and how does the order of source command in .bashrc affect? I am wondering. 
 

On Thu, Jul 21, 2011 at 11:29 AM, Francois Berenger <berenger@riken.jp> wrote:
I have this in my .bashrc, I use the command phenix_setup
only before I start using phenix:

---
# to use locally installed phenix
function phenix_setup() {
   PHENIX_ENV=\
/usr/local/phenix-dev/phenix-dev-756/phenix-dev-756/phenix_env.sh
   if [ -f $PHENIX_ENV ]; then
       source $PHENIX_ENV
   fi
}
---

I use the same kind of trick for CCP4.

PS: You need to adapt this code to where your
   phenix_env.sh is installed.


On 07/21/2011 06:20 PM, G P wrote:
Hi Ralf,

Thanks a lot for your help. I changed the order and it works now. But I
am wondering why? Is that means the .bashrc script will read lines from
down to up which allow it to see the line of source for phenix first?

Thanks a lot again!

cheers,
GP

On Wed, Jul 20, 2011 at 10:35 PM, Ralf Grosse-Kunstleve
<rwgrosse-kunstleve@lbl.gov <mailto:rwgrosse-kunstleve@lbl.gov>> wrote:

   Hopefully, all you need to do is source phenix_env last.
   E.g. look in your .cshrc or .bashrc file with the phenix and ccp4
   source commands.
   Reorder the commands so that phenix comes after the ccp4 command.
   Then open a new shell and run "phenix.phaser params.eff" again.
   Could you try that?
   (I recommend against copying files from the phenix to the ccp4 tree.)
   Ralf

   On Wed, Jul 20, 2011 at 11:21 AM, G P <gysubscribe@gmail.com
   <mailto:gysubscribe@gmail.com>> wrote:

       Dear all,

       It's long story:

       At beginning, I have phenix installed. I do not have CCP4
       installed. Then I run "phenix.phaser params.eff" to call phenix
       run phaser from script params.eff. It works well.
       Then, I installed CCP4 with its own phaser inside. Then I run
       again "phenix.phaser params.eff". The computer start to import
       files (should be some libraries and supporting files, not input
       data) from CCP4 installation directory. It seems so strange for me.

       And because some of the .so files in CCP4 directory are for
       32bit, phenix.phaser gave me error message: wrong ELF class:
       ELFCLASS32 and refused to keep running. I guess I could solve
       this problem by copying the same .so file in phenix directory
       into CCP4's directory.

       What I really want to know is why this happen. Is that the
       installation of CCP4 changed some kinds of PATH variables for
       phenix? How could I fix by giving a right path again?

       I would appreciate to any help. Thanks a lot guys!

       Best regards,
       GP


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