<div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Hi Roberto,<div><br></div><div>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</div><div><br></div><div><font face="monospace, monospace">phenix.validation_cryoem <path to>/5ni1.cif <path to>/molprobity.mrc resolution=2.2</font></div><div><br></div><div>The resolution is required. If you have half-maps, you will have to specify them like</div><div><br></div><div><span style="font-family:monospace,monospace">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</span><br></div><div><br></div><div>To see all the available options, you can type<br></div><div><br></div><div><font face="monospace, monospace">phenix.validation --show-defaults=3</font></div><div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Let us know if you have any other questions. Thanks!</div><div><br></div><div><div><div dir="ltr" class="gmail-m_-5492614197102727872m_-5930242892412385230gmail-m_44541867891945646gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div>--</div><div><span style="font-size:12.8000001907349px">Billy K. Poon</span><br></div></div><div>Research Scientist, Molecular Biophysics and Integrated Bioimaging</div><div>Lawrence Berkeley National Laboratory</div><div>1 Cyclotron Road, M/S 33R0345</div><div>Berkeley, CA 94720</div><div>Tel: (510) 486-5709</div><div>Fax: (510) 486-5909</div><div>Web: <a href="https://phenix-online.org" target="_blank">https://phenix-online.org</a></div></div></div></div></div></div></div></div></div></div></div></div></div></div><br></div></div></div></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Feb 25, 2019 at 2:46 AM Roberto Marabini <<a href="mailto:roberto@cnb.csic.es" target="_blank">roberto@cnb.csic.es</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr">Hi,<div><br></div><div> In the past (phenix 1.13) I have been able to execute molprobity with the command line:</div><div><br></div><div>==============</div><div>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<br></div><div>==================</div><div><br></div><div>Unfortunately, for version 1.14 I get the error:</div><div><br></div><div>==========================</div><div><div> Traceback (most recent call last):</div><div> File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 310, in <module></div><div> run(sys.argv[1:])</div><div> File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/command_line/molprobity.py", line 193, in run</div><div> map_params=params)</div><div> File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/molprobity/__init__.py", line 216, in __init__</div><div> molprobity_map_params=map_params.input.maps)</div><div> File "/usr/local/phenix-1.14-3260/modules/cctbx_project/mmtbx/validation/experimental.py", line 198, in __init__</div><div> from mmtbx.command_line.map_model_cc import get_fsc</div><div> ImportError: No module named map_model_cc</div></div><div>==============</div><div><br></div><div>That is, there is an error in the line</div><div><br></div><div> "from mmtbx.command_line.map_model_cc import get_fsc"</div><div><br></div><div>By the way, if I just run the command:</div><div><br></div><div><div>==============</div><div>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 <br></div><div>==================</div><div><br></div><div>the program is executed without any problem.</div><div><br></div><div>What should I do in order to execute molprobity.py with the option map_file_name.</div><div><br></div><div> best wishes</div><div><br></div><div> Roberto</div><div><br></div><br class="gmail-m_-5492614197102727872gmail-m_-5930242892412385230gmail-m_44541867891945646gmail-m_9005853273886627234gmail-Apple-interchange-newline"></div></div></div></div></div></div>
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