[phenixbb] phenix.molprobity geo

[Paul Emsley]

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-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 
> <mailto: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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