[phenixbb] phenix.molprobity geo

[Christopher Williams]

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 <pemsley at mrc-lmb.cam.ac.uk>
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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