[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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