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


On Mon, Feb 25, 2019 at 2:46 AM Roberto Marabini <roberto@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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