<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">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">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">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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