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= half_map= 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 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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