mmtbx.command_line.mask (phenix.mask) doesn't work

[wojdyr]

Hello,

When I tried to run a shell script from a few years ago I got such an error:

$ cctbx.python -m mmtbx.command_line.mask aa.pdb 
-------------------------------------------------------------------------------
phenix.mask: Given PDB file calculate bulk-solvent mask

How to run:
  phenix.mask model.pdb

-------------------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/wojdyr/miniforge3/lib/python3.10/runpy.py", line 196, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/home/wojdyr/miniforge3/lib/python3.10/runpy.py", line 86, in _run_code
    exec(code, run_globals)
  File "/home/wojdyr/miniforge3/lib/python3.10/site-packages/mmtbx/command_line/mask.py", line 53, in <module>
    run(args=sys.argv[1:])
  File "/home/wojdyr/miniforge3/lib/python3.10/site-packages/mmtbx/command_line/mask.py", line 44, in run
    mmtbx_masks_asu_mask_obj = mmtbx.masks.asu_mask(
TypeError: asu_mask.__init__() got an unexpected keyword argument 'n_real'

The signature of asu_mask.__init__() seem to has changed. The calling function was updated for example here: https://github.com/cctbx/cctbx_project/commit/2243cc9a24bc06c7f89ff3a5e927777a781121fa#diff-3f3f745e29616712b7e173ed18e25c5aaf137093fac8dec9189fdcfe69c1942d but not here: https://github.com/cctbx/cctbx_project/blob/4149890d6c5b6d9c4906d744553190bfa9c493d5/mmtbx/command_line/mask.py#L44-L46

[dcliebschner]

This should be fixed now.

[bkpoon]

You can try the fix in the nightly builds of the conda packages (only the most recent 5 builds are available, https://anaconda.org/cctbx-nightly/cctbx-base). You can try this command to update the cctbx-base in your active conda environment.

conda update -c cctbx-nightly cctbx-base

The update command should work with the latest build of cctbx-base from conda-forge. There was a change in the Boost libraries relatively recently, so if your environment has boost and boost-cpp, the update command may not work or may pick an earlier nightly build.

Alternatively, you can create a new environment with

conda create -n new_environment -c cctbx-nightly -c conda-forge cctbx-base

This will pull cctbx-base from the nightly build channel and all the other dependencies from conda-forge.

[wojdyr]

Thanks! I just forgot to close this issue.

[bkpoon]

No worries! The next release on conda-forge will have the fix.