Hi Christopher, Thanks for your informative and prompt reply. On reexamining the output, I think then that I misunderstood the output. The NBCs listed below are from *refinement* analysis, not molprobity analysis. I was mislead because there were no NBCs listed in the Molprobity part of the log file. Yes, you are right, the output of phenix.clashscore was what I actually wanted, not phenix.molprobity and a .geo file. Regards, Paul. On 04/03/2021 18:51, Christopher Williams wrote:

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-restr...) 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 mailto:[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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