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ReliaSolve / Molprobity2

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Learn to produce the "RNA backbone" number on the PDB page for a molecule #132

Closed russell-taylor closed 3 years ago

russell-taylor commented 3 years ago

Find out how to run SuiteName on PDB files to produce the "RNA backbone" number on the PDB page to check that we're able to reproduce it with SuiteName before talking with the PDB folks about upgrading.

russell-taylor commented 3 years ago

MolProbity does the following to get the intermediate file from a model file to send to SuiteName: mmtbx.mp_geo rna_backbone=True F:/data/Richardsons/4z4d.cif

russell-taylor commented 3 years ago

It then runs the following, piping the output of the above into this command, to get the results: phenix.suitename -string -oneline -pointIDfields 7 -altIDfield 6 It pipes the output to fold -w 60

russell-taylor commented 3 years ago

The complete report from this molecule (click on the summary graph) shows Mol 2 chain B analyzed 18/21 and 3 D 7/11 with no RNA backbone outliers and no RNA pucker outliers. Its summary score was 0.69.

russell-taylor commented 3 years ago

When running the original SuiteName with -report rather than -string, we get "For all 25 suites: average suiteness== 0.687 (power==3.00)", which is consistent with the 0.69 value reported above.