[phenixbb] molprobity in phenix 1.14

[Billy Poon]

Hi Roberto,

The validation of models and real-space maps has been consolidated into the
phenix.validation_cryoem tool. To run from the command-line, you would type

phenix.validation_cryoem <path to>/5ni1.cif <path to>/molprobity.mrc
resolution=2.2

The resolution is required. If you have half-maps, you will have to specify
them like

phenix.validation_cryoem <path to>/5ni1.cif full_map=<path
to>/molprobity.mrc half_map=<path to half map 1> half_map=<path to half map
2> resolution=2.2

To see all the available options, you can type

phenix.validation --show-defaults=3

The "3" shows the advanced parameters as well and will show that
"pdb_interpretation.clash_guard.nonbonded_distance_threshold" is set to
"None" by default. The "nproc" parameter is available as "mtriage.nproc"
and "ss_validation.nproc". For very large structures, the nproc parameter
may improve performance because the secondary structure annotations can be
validated separately.

Also, instead of calling "phenix.python <path to>/molprobity.py," you can
just call "phenix.molprobity". The plan is for the code in
phenix.molprobity to be reorganized to be similar to
phenix.validation_cryoem so this specific bug may not be fixed until then.

Let us know if you have any other questions. Thanks!

--
Billy K. Poon
Research Scientist, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
1 Cyclotron Road, M/S 33R0345
Berkeley, CA 94720
Tel: (510) 486-5709
Fax: (510) 486-5909
Web: https://phenix-online.org


On Mon, Feb 25, 2019 at 2:46 AM Roberto Marabini <roberto at cnb.csic.es>
wrote:

> Hi,
>
>   In the past (phenix 1.13) I have been able to execute molprobity with
> the command line:
>
> ==============
> phenix.python
> /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py
> /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif
> map_file_name=/home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/molprobity.mrc
> d_min=2.200000 pickle=True
> pdb_interpretation.clash_guard.nonbonded_distance_threshold=None   nproc=4
> pdb_interpretation.clash_guard.nonbonded_distance_threshold=None
> ==================
>
> Unfortunately, for version 1.14 I get the error:
>
> ==========================
>  Traceback (most recent call last):
>  File
> "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py",
> line 310, in <module>
>     run(sys.argv[1:])
>     File
> "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py",
> line 193, in run
>       map_params=params)
>      File
> "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/molprobity/__init__.py",
> line 216, in __init__
>       molprobity_map_params=map_params.input.maps)
>     File
> "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/experimental.py",
> line 198, in __init__
>      from mmtbx.command_line.map_model_cc import get_fsc
>    ImportError: No module named map_model_cc
> ==============
>
> That is, there is an error in the line
>
>      "from mmtbx.command_line.map_model_cc import get_fsc"
>
> By the way, if I just run the command:
>
> ==============
> phenix.python
> /usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py
> /home/roberto/sda/ScipionUserData/projects/TestMolprobityValidation2/Runs/000170_PhenixProtRunMolprobity/extra/5ni1.cif
> ==================
>
> the program is executed without any problem.
>
> What should I do in order to execute  molprobity.py with the
> option  map_file_name.
>
>   best wishes
>
>               Roberto
>
>
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