[phenixbb] geometry_minimization makes molprobity score worse
James Holton
jmholton at lbl.gov
Wed Jul 7 20:58:11 PDT 2021
Greetings all, and I hope this little observation helps improve things
somehow.
I did not expect this result, but there it is. My MolProbity score goes
from 0.7 to 1.9 after a run of phenix.geometry_minimization
I started with an AMBER-minimized model (based on 1aho), and that got me
my best MolProbity score so far (0.7). But, even with hydrogens and
waters removed the geometry_minimization run increases the clashscore
from 0 to 3.1 and Ramachandran favored drops from 98% to 88% with one
residue reaching the outlier level.
Just for comparison, with refmac5 in "refi type ideal" mode I see the
MolProbity rise to 1.13, but Clashscore remains zero, some Ramas go from
favored to allowed, but none rise to the level of outliers.
Files and logs here:
https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz
I suspect this might have something to do with library values for
main-chain bonds and angles? They do seem to vary between programs.
Phenix having the shortest CA-CA distance by up to 0.08 A. After running
thorough minimization on a poly-A peptide I get:
bond amber refmac phenix shelxl Stryer
C-N 1.330 1.339 1.331 1.325 1.32
N-CA 1.462 1.482 1.455 1.454 1.47
CA-C 1.542 1.534 1.521 1.546 1.53
CA-CA 3.862 3.874 3.794 3.854
So, which one is "right" ?
Cheers,
-James
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