phenix.real_space_refine
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I tried to run the phenix.real_space_refine that was discussed in the CCN but I get the following error. import mmtbx.refinement.real_space.driver ImportError: No module named driver I downloaded the latest nightly build dev-1463. Even when asking for the help I get the same error. I did however successfully create some FEMs which look lovely. Heather Condurso UF-Department of Chemistry [email protected]
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Hi Heather,
I tried to run the phenix.real_space_refine that was discussed in the CCN but I get the following error.
import mmtbx.refinement.real_space.driver ImportError: No module named driver
I downloaded the latest nightly build dev-1463.
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..
I did however successfully create some FEMs which look lovely.
I'm glad to hear this! All the best, Pavel
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On Fri, Aug 23, 2013 at 12:14 AM, Pavel Afonine
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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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: [email protected] or [email protected] ------------------------------------------------------------------------------- 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
mailto:[email protected]> 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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participants (3)
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Heather L Condurso
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Nathaniel Echols
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Pavel Afonine