[phenixbb] phenix.real_space_refine

[Pavel Afonine]

Yes, this is true... I deleted mmtbx.refinement.real_space.driver a 
while ago. Interesting, it still works for me because I still have 
../sources/cctbx_project/mmtbx/refinement/real_space/driver.pyc

Once I deleted .pyc file it stopped working:

marbles:/net/marbles/raid1/afonine/build % phenix.real_space_refine
-------------------------------------------------------------------------------
Initialization, inputs
**********************
-------------------------------------------------------------------------------
phenix.real_space_refine: tool for extensive real-space refinement of atomic
                           coordinates against provided map

Usage:
   phenix.real_space_refine model.pdb ccp4_formatted_map.map
   or
   phenix.real_space_refine model.pdb map.mtz
   or
   phenix.real_space_refine model.pdb map.mtz label='2FOFCWT,PH2FOFCWT'

Feedback:
   PAfonine at lbl.gov or phenixbb at phenix-online.org
-------------------------------------------------------------------------------
marbles:/net/marbles/raid1/afonine/build % rm -rf 
../sources/cctbx_project/mmtbx/refinement/real_space/driver.pyc
marbles:/net/marbles/raid1/afonine/build % phenix.real_space_refine
Traceback (most recent call last):
   File 
"/net/marbles/raid1/afonine/build/../sources/phenix/phenix/command_line/real_space_refine.py", 
line 20, in <module>
     import mmtbx.refinement.real_space.driver
ImportError: No module named driver
marbles:/net/marbles/raid1/afonine/build %

Quite a trap! Will be fixed in a next build. Thanks for catching this.

Pavel


On 8/23/13 7:44 AM, Nathaniel Echols wrote:
> On Fri, Aug 23, 2013 at 12:14 AM, Pavel Afonine <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> wrote:
>
>     are you sure you are using the latest (dev-1463) nightly build? I
>     just tried phenix.real_space_refine using dev-1463 and it worked
>     fine. Could it be you have multiple versions installed and by
>     accident you used a wrong one? What was the exact command that
>     crashed with the above error message? Just throwing random
>     guesses/questions to see what's gone wrong..
>
>
> It's not working for me either; the module being referenced has been 
> deleted:
>
> chevy:~ % source /net/chevy/raid1/phenix/phenix-dev-1463/phenix_env
> chevy:~ % phenix.real_space_refine
> Traceback (most recent call last):
>   File 
> "/net/chevy/raid1/phenix/phenix-dev-1463/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/real_space_refine.py", 
> line 20, in <module>
>     import mmtbx.refinement.real_space.driver
> ImportError: No module named driver
>
> It was removed in CCTBX revision 17833:
>
> http://sourceforge.net/p/cctbx/code/17833/
>
> -Nat
>
>
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> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

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