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<p>Hi Christopher,</p>
<p>Thanks for your informative and prompt reply.</p>
<p>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.</p>
<p>Yes, you are right, the output of phenix.clashscore was what I
actually wanted, not phenix.molprobity and a .geo file.</p>
<p>Regards,<br>
</p>
<p>Paul.</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 04/03/2021 18:51, Christopher
Williams wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAAhO6EiVRu5VYDPjkPJdbpnNXBJSuJQqkHn4BwUz9MQrgZ123Q@mail.gmail.com">
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<div dir="ltr">
<div>Hi Paul,</div>
<div><br>
</div>
<div>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 (<a
href="https://www.phenix-online.org/documentation/file_formats.html#geometry-restraints-info-geo"
moz-do-not-send="true">https://www.phenix-online.org/documentation/file_formats.html#geometry-restraints-info-geo</a>)
and this newsletter article (<a
href="http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10"
moz-do-not-send="true">http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10</a>)
mention this method of generation.</div>
<div><br>
</div>
<div>However, you can generate a geo file directly from a model
with this commandline:</div>
<div>phenix.pdb_interpretation <i>your_model.pdb</i>
write_geo_files=True</div>
<div>This is probably the more useful option for your purposes.<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>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.<br>
</div>
<div><br>
</div>
<div>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.<br>
</div>
<div><br>
</div>
<div>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.<br>
</div>
<div><br>
</div>
<div>Hopefully someone with a better understanding of the
nonbonded distances will be able to chime in with a better
explanation.</div>
<div><br>
</div>
<div>Good luck,</div>
<div>-Christopher Williams</div>
<div>---Richardson Lab, Duke University</div>
<div><br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Mar 4, 2021 at 1:00 PM
Paul Emsley <<a href="mailto:pemsley@mrc-lmb.cam.ac.uk"
moz-do-not-send="true">pemsley@mrc-lmb.cam.ac.uk</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hello,<br>
<br>
<br>
I'd like to compare the restraints generated by Coot to the
validation <br>
provided by molprobity. When I run phenix.molprobity on my
model, it <br>
gives me (amongst other things) this:<br>
<br>
-----------------------<br>
<br>
Histogram of nonbonded interaction distances:<br>
1.87 - 2.42: 526<br>
2.42 - 2.96: 3217<br>
2.96 - 3.51: 3639<br>
3.51 - 4.05: 5026<br>
4.05 - 4.60: 6847<br>
Nonbonded interactions: 19255<br>
Sorted by model distance:<br>
nonbonded pdb=" O LEU A 21 "<br>
pdb=" H GLY A 26 "<br>
model vdw<br>
1.874 1.850<br>
nonbonded pdb=" H ILE A 71 "<br>
pdb=" O TYR A 80 "<br>
model vdw<br>
1.920 1.850<br>
nonbonded pdb=" H GLY A 34 "<br>
pdb=" O GLU A 54 "<br>
model vdw<br>
1.925 1.850<br>
nonbonded pdb=" O ILE A 71 "<br>
pdb=" H TYR A 80 "<br>
model vdw<br>
1.937 1.850<br>
nonbonded pdb=" HE ARG A 40 "<br>
pdb=" HG1 THR A 76 "<br>
model vdw sym.op.<br>
1.955 2.100 -x+3/2,-y,z+1/2<br>
... (remaining 19250 not shown)<br>
<br>
NOTE: a complete listing of the restraints can be obtained
by requesting<br>
output of .geo file.<br>
--------------------------<br>
<br>
<br>
I don't understand this lilst. Should I be concerned by those
<br>
interactions? Which of these atom pairs are contributing to
the clashscore?<br>
<br>
Perhaps the details are in the .geo file? How do I get a .geo
file? I <br>
googled, I didn't find the answer. How could I have found the
answer <br>
without asking here?<br>
<br>
<br>
Thanks,<br>
<br>
Paul.<br>
<br>
<br>
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