Different scoring applications (score vs score_aln vs score_jd2, etc.)?

[Anonymous]

What’s the difference between the different scoring applications?

In my bin folder I find the following scoring applications:

score, score_aln, score_aln2, score_jd2.

What’s the difference between them?

(I am omitting the trailing .default.linuxgccrelease, or mpi.linuxgccrelease, since I know those denote parallel vs non-parallel versions)

[Anonymous]

The score_aln and score_aln2 applications are specialist ones which score *alignments* rather than structures.

Both score and score_jd2 score structures. The primary difference between them is their input/output options. score_jd2 uses the standard “JD2” input/output options that a large number of Rosetta applications use. The score application is an older application which has its own idiosyncratic input/output options. (Though most of the major ones match.)

The other practical difference is that the score application currently has better support for calculating rmsd. (Providing -in:file:native with the score application will result in rmsd columns in the output, though with score_jd2 it doesn’t necessarily.)

[Anonymous]

Thanks for the reply. That clears up things.

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