I'm new to Rosetta and currently working through the tutorials.
I often recognized that the the score values produced by the recent version "Rosetta 2019.47" on my computer differ from the ones cited in the tutorials and given expected_output.
in the Scoring Tutorial (subchapter "Changing the Score Function") the command
-in:file:l input_files/pdblist -score:weights docking -out:file:scorefile output_files/score_docking.sc
delivers the following score.sc-files:
SEQUENCE: SCORE: total_score score dslf_ca_dih dslf_cs_ang dslf_ss_dih dslf_ss_dst fa_atr fa_dun fa_elec fa_pair fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb linear_chainbreak overlap_chainbreak time description SCORE: -111.103 -111.103 0.000 0.000 0.000 0.000 -169.606 5.373 -3.798 -2.237 5.683 73.720 -0.822 -8.609 -2.680 -8.128 0.000 0.000 0.000 1qys_0001 SCORE: -83.850 -83.850 0.000 0.000 0.000 0.000 -131.980 4.479 -3.295 -2.059 3.845 58.363 -1.663 -5.786 -1.092 -4.661 0.000 0.000 0.000 1ubq_0001
while expected output file says:
SEQUENCE: SCORE: total_score score dslf_ca_dih dslf_cs_ang dslf_ss_dih dslf_ss_dst fa_atr fa_dun fa_elec fa_pair fa_rep fa_sol hbond_bb_sc hbond_lr_bb hbond_sc hbond_sr_bb linear_chainbreak overlap_chainbreak time description SCORE: -89.596 -89.596 0.000 0.000 0.000 0.000 -143.190 5.640 -1.371 -2.577 3.929 62.290 -0.824 -5.653 -2.502 -5.338 0.000 0.000 0.000 1qys_0001 SCORE: -55.214 -55.214 0.000 0.000 0.000 0.000 -119.403 4.578 -1.412 -2.044 10.233 66.103 -3.048 -3.799 -3.360 -3.061 0.000 0.000 0.000 1ubq_0001
As the tutorials say that the locally calculated scores should be the same as in the tutorial, I am now uncertain if these deviations occure due to a wrong software usage of mine or weather Rosetta's scoring functions could have changed since the tutorial was written.
It would be great if someone could help me with this question.
(btw, if it's interesting for anyone: Rosetta seems not to run automatically on the latest Ubuntu 19.10 distribution. The terminal says something about that the GCC is no longer supported. First I (also new to Linux) was insecure because somewhere I read that on Ubuntu it's not necessary to install additional compilers. Anyway I could build the software using a MX Linux 19.0 distribution)
You're correct that the scorefunction behavior has changed since the tutorial has been written. The current default scorefunction environment for recent versions of Rosetta is REF2015. Now while there's a weights file with this name, the changes which made REF2015 are more than just the weights file. There's additional underlying behavior which was changed when moving to REF2015, and this is also reflected in the scorefunctions which aren't REF2015.
I think you're running into that here. The tutorial was written before we switched to REF2015, and as such the example outputs are using a slightly different scorefunction. (docking weights in a talaris environment versus docking weights in a REF2015 environment) I wouldn't be too concerned about a difference in scoring here.
Thanks for your answer. Since the most tutorials were written around 2016 and as REF2015 is also mentioned in the scoring tutorial, I assuemd that REF2015 scorefunction was used in all the tutorials. But as far as I understand there were also changes in the software offside the REF2015-function that contribute can contribute to slightly different resultas.
Anyway I'm now more concernd about differences in pdb files originated from tutorial's tasks.
For example in the Fold-tree-tutorial the given command
delivers a pdb-structure that has big differences to the example outputs shown in the tutorial. On top of that, the tutorial's next command
which runs the same relax protocol, but from the opposite direction in terms of C- and N-termina, produces nearly the same structure as the first command.
To show this I will share the two pdb-files originated from these two commands: