Score – Strange message

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    • #1762

        When I was trying to rescore and combine a list of PDB files which were created by loop modeling with the score application I get the following message:
        hey is this the right thing to be doing???

        It seems that the silent file is OK, as well as the score file. Does this message mean anything?
        Google wasn’t very helpful, only a BOINC/Rosetta@home user with the same message.

        The command I was using:
        score.linuxgccrelease -in:file:l filelist_all.txt -database rosetta_database -rescore:verbose true -score:weights membrane_highres_Menv_smooth.wts -in:file:spanfile span.txt -out:file:scorefile score.txt -out:file:silent silent.out -out:file:silent_struct_type binary

      • #9515

          That message comes up during rmsd evaluation. Specifically it comes about during the case where the first two eigenvalues are degenerate when calculating the rotational component of the transform for the rmsd calculation. Instead of basing the calculations off of the first two eigenvectors, it bases it off of the second and third (which aren’t degenerate).

          The “is this the right thing” is in reference to the internal code, rather than a reference to anything you’re doing. Unless you’re an rmsd wonk, and are particular about how the numbers are being calculated, you can safely ignore it.

        • #9516

            That’s interesting….

            I didn’t calculate the RMSD since I don’t have a native structure.

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