Hi Paul,

As I understand it, a .geo file is most usually produced as one of the outputs of refinement. A few different places, such as this documentation (https://www.phenix-online.org/documentation/file_formats.html#geometry-restraints-info-geo) and this newsletter article (http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10) mention this method of generation.

However, you can generate a geo file directly from a model with this commandline:

phenix.pdb_interpretation your_model.pdb write_geo_files=True

This is probably the more useful option for your purposes.

For understanding clashes, I recommend running phenix.clashscore and using its dedicated and complete output. This will return a list of all the clashes, sorted in order of severity.

As to non-bonded interaction distances, I believe that they are close approaches between atoms that are not covalently bonded. As you can see from the histogram bins (1.87 - 2.42, 2.42 - 2.96, 2.96 - 3.51, 3.51 - 4.05, 4.05 - 4.60A), these distances do not necessarily indicate clashes, but instead cover a range of distances in the general vdW contact region. The distribution of this histogram gives a general sense of how well packed the model is.

Very close non-bonded interactions may register as clashes in Probe and/or may generate various error messages in Phenix depending on your options. For various reasons, there is not an exact mapping between close non-bonded interactions and clashes.

Hopefully someone with a better understanding of the nonbonded distances will be able to chime in with a better explanation.

Good luck,

-Christopher Williams

---Richardson Lab, Duke University

On Thu, Mar 4, 2021 at 1:00 PM Paul Emsley <[email protected]> wrote:

Hello,

I'd like to compare the restraints generated by Coot to the validation
provided by molprobity. When I run phenix.molprobity on my model, it
gives me (amongst other things) this:

-----------------------

   Histogram of nonbonded interaction distances:
         1.87 -     2.42: 526
         2.42 -     2.96: 3217
         2.96 -     3.51: 3639
         3.51 -     4.05: 5026
         4.05 -     4.60: 6847
   Nonbonded interactions: 19255
   Sorted by model distance:
   nonbonded pdb=" O   LEU A 21 "
             pdb=" H   GLY A 26 "
      model   vdw
      1.874 1.850
   nonbonded pdb=" H   ILE A 71 "
             pdb=" O   TYR A 80 "
      model   vdw
      1.920 1.850
   nonbonded pdb=" H   GLY A 34 "
             pdb=" O   GLU A 54 "
      model   vdw
      1.925 1.850
   nonbonded pdb=" O   ILE A 71 "
             pdb=" H   TYR A 80 "
      model   vdw
      1.937 1.850
   nonbonded pdb=" HE ARG A 40 "
             pdb=" HG1 THR A 76 "
      model   vdw sym.op.
      1.955 2.100 -x+3/2,-y,z+1/2
   ... (remaining 19250 not shown)

   NOTE: a complete listing of the restraints can be obtained by requesting
         output of .geo file.
--------------------------

I don't understand this lilst. Should I be concerned by those
interactions? Which of these atom pairs are contributing to the clashscore?

Perhaps the details are in the .geo file? How do I get a .geo file? I
googled, I didn't find the answer. How could I have found the answer
without asking here?

Thanks,

Paul.

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