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 < [email protected]> 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 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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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 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 >> 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 mailto:[email protected]**> 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

______________________________**_________________ phenixbb mailing list [email protected]

...

http://phenix-online.org/**mailman/listinfo/phenixbbhttp://phenix-online.org/mailman/listinfo/phenixbb

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...

http://phenix-online.org/**mailman/listinfo/phenixbbhttp://phenix-online.org/mailman/listinfo/phenixbb

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To add to the information provided by Francois and Ed: The .bashrc file is read only when a new shell is started (not each time you execute a command). The source phenix_env.sh command prepends an entry to PATH. To see the result try: echo $PATH This PATH determines the order in which commands are found. If you have phenix.phaser in PHENIX and another one in CCP4, you can determine which one is used by the order in which the phenix and ccp4 directories appear in $PATH. Ralf On Thu, Jul 21, 2011 at 2:20 AM, 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 < [email protected]> 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 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

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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