[phenixbb] phenix.molprobity geo

Paul Emsley pemsley at mrc-lmb.cam.ac.uk
Thu Mar 4 09:59:40 PST 2021


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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