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)
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.)
Thanks for the reply. That clears up things.
Where can I acess score_jd2 algoritm for more details?
I found a briefly description here too: https://www.rosettacommons.org/docs/latest/application_documentation/membrane_proteins/RosettaMP-App-MPScoring. But it isn''t enought.
I can't found the respective score_jd2 script on source download to visualize the algoritm like when we want to visualize some script in Python.
The program score_jd2 packing residue that has missing atoms. What else?