[phenixbb] phenix.molprobity geo
pemsley at mrc-lmb.cam.ac.uk
Thu Mar 4 11:35:16 PST 2021
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.
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
> 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
> 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
> <mailto:pemsley at mrc-lmb.cam.ac.uk>> wrote:
> I'd like to compare the restraints generated by Coot to the
> 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
> 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
> 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?
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