[phenixbb] get list of missing atoms table in validation

Billy Poon BKPoon at lbl.gov
Thu May 5 15:23:14 PDT 2022

Hi Wei,

Yes, but you would need to open the pickle file that stores the results for
the job.

The pickle file is stored in the same directory as the job parameters. If
you select a job and click on "Show details" on the bottom, you'll get a
dialog that shows the relative path to the "Config file". The corresponding
pickle file is that name, but replace the ".eff" extension with ".pkl". The
full path to the file can be constructed by combining the "Directory" field
with the "Config file" field. Basically, your project directory has a
hidden ".phenix" directory that stores the outputs for each job in the

Once you know where the pickle file is, you can run the following code to
print out the list of missing atoms.

import sys
from libtbx import easy_pickle

if __name__ == '__main__':

  # for simplicity, assume the first argument is the result pickle
  assert len(sys.argv) == 2
  p = easy_pickle.load(sys.argv[1])
  validation = p.validation
  missing_atoms = p.validation.missing_atoms

  # print missing atoms
  # the first column is the chain
  # the second column is the residue (name and number)
  # the third column is the altloc
  # the fourth column is the atom name
  # the remaining columns are extra information (selection string and
  for missing_atom in missing_atoms:

So if you save the code in a text file named "extract_missing_atoms.py",
you would run the code by typing

libtbx.python extract_missing_atoms.py <pickle file>

This will work with a validation job (molprobity_<job number>.pkl) as well
as a phenix.refine job (refine_<job number>.pkl). Let me know if you run
into any issues.

This is something that we plan on addressing as we work on a new GUI. There
are some additions to the Cryo-EM validation GUI where there is an "Export
data" button for exporting the data for some of the graphs.

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

On Wed, May 4, 2022 at 2:17 PM Wei Wang <ww2283 at columbia.edu> wrote:

> Dear all,
> I would like to get an externally readable list of the *missing atoms* table
> in “*Summary*" session of "*Comprehensive validation (X-ray/Neutron)*".
> Currently it seems the information is integrated and clickable only inside
> the gui window. I want to access the table via sed. Is there a way to
> extract that table out?
> Best regards,
> Wei
> _______________________________________________
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> phenixbb at phenix-online.org
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