[phenixbb] python issues

Mark Brooks mark.x.brooks at gmail.com
Tue Mar 9 14:56:06 PST 2010


Hi,
   Are you sure the error is from CCP4, and not Phenix? I got this error
from installing Phenix badly (IIRC).

Did you install Phenix by just moving the directory from one system to
another, but which also involved changing the path? If so, it's easiest to
re-run the installer:

./install --prefix=/where/you/want/to/install/phenix

http://www.phenix-online.org/pipermail/phenixbb/2008-January/000689.html

Otherwise, copying the entire directory tree, but keeping the paths the
same on all systems worked for me when installing on multiple systems.

HTH

Mark
P.S. The configure.py to run would be "/cctbx_project/libtbx/configure.py"
from PHENIX in that case, I guess.

On 9 March 2010 22:01, Patrick Loll <pat.loll at drexel.edu> wrote:

> Hi,
>
> This is really a ccp4-provoked question, but it relates to phaser & cctbx
> (I think), so I'll try here as well:
>
> After an install of ccp4 on a MacBook Pro running Snow Leopard and on a
> MacPro running Leopard, the command:
>
> source /sw*/bin/init.csh       (where /sw* is either /sw64 on the machine
> running 10.6, or /sw on the machine running 10.5)
>
> gives the error:
>
>    *******************************************
>    Fatal Error: Incomplete libtbx environment!
>    *******************************************
>    Please re-run the libtbx/configure.py command.
>
>
>
> If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type
>
> python configure.py
>
> Then it tells me that the md5 module is deprecated, and that the cool kids
> use hashlib instead.  Does this mean that I need to go to an earlier version
> of python?  Will that mess up other things?
>
> Curiously, one machines giving this problem has python 2.5.1, while the
> other has 2.6.  However, I currently have python 2.5.1 running on another
> machine (albeit with a slightly earlier version of ccp4) and it doesn't give
> me this problem.
>
> Ideas?
>
> Thanks,
>
> Pat
>
>
> ---------------------------------------------------------------------------------------
>
> Patrick J. Loll, Ph. D.
>
> Professor of Biochemistry & Molecular Biology
>
> Director, Biochemistry Graduate Program
>
> Drexel University College of Medicine
>
> Room 10-102 New College Building
>
> 245 N. 15th St., Mailstop 497
>
> Philadelphia, PA  19102-1192  USA
>
>
> (215) 762-7706
>
> pat.loll at drexelmed.edu
>
>
> _______________________________________________
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> http://phenix-online.org/mailman/listinfo/phenixbb
>
>


-- 
Skype: markabrooks
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