(relevant files can be downloaded at https://copy.com/yOhxRslZzK8j9z0l)
Dear friends,
In the instructions about ddg_monomer,
https://www.rosettacommons.org/docs/latest/ddg-monomer.html
it is mentioned that "the most accurate ddG is taken as the difference between the mean of the top-3-scoring wild type structures and the top-3-scoring point-mutant structures".
In my "ddg_predictions.out", the "total" term seems to indicate a ddG of 1.247.
However, after using score_jd2.linuxgccrelease to score the "wt_.out" and "mut_A111C.out", "total_score" and "score" are shown for all the 50 trajectories. Afterwards, I rank those 50 trajectories in "wt_.out" and "mut_A111C.out", and calculate "the difference between the mean of the top-3-scoring wild type structures and the top-3-scoring point-mutant structures". What I got is:
For "total_score":
(-723.7-723.59-723.301)/3-(-724.728-723.934-723.709)/3=0.593
For "score":
(-1096.21-1096.104-1095.652)/3-(-1097.457-1096.407-1096.143)/3=0.680
As you can see, neither 0.593 nor 0.680 is identical to 1.247.
So can I ask what is the exact scorefunction ddg_monomer uses to calculate the "total" term in "ddg_predictions.out"?
Thank you very much.
Yours sincerely
Cheng
Your ddg_monomer scoring function appears to have been talaris2013, To go into detail, your log output displays the following scoring terms and weights (for an example state).
------------------------------------------------------------
Scores Weight Raw Score Wghtd.Score
------------------------------------------------------------
fa_atr 0.800 -2823.941 -2259.152
fa_rep 0.440 543.884 239.309
fa_sol 0.750 1545.485 1159.114
fa_intra_rep 0.004 828.621 3.314
fa_elec 0.700 -249.860 -174.902
pro_close 1.000 1.635 1.635
hbond_sr_bb 1.170 -34.251 -40.073
hbond_lr_bb 1.170 -144.095 -168.591
hbond_bb_sc 1.170 -45.162 -52.839
hbond_sc 1.100 -31.661 -34.827
dslf_fa13 1.000 -3.033 -3.033
atom_pair_constraint 1.000 8.692 8.692
rama 0.200 -102.002 -20.400
omega 0.500 64.018 32.009
fa_dun 0.560 549.834 307.907
p_aa_pp 0.320 -228.629 -73.161
ref 1.000 25.170 25.170
---------------------------------------------------
Total weighted score: -1049.829
Looking at your scoring output, you were also using talaris2013 for scoring. Notably, the final lines of log output are
protocols.moves.ddGMover: mutate A111C wildtype_dG is: -1097.46 and mutant_dG is: -1096.21 ddG is: 1.24653
apps.public.ddg.ddg_monomer: mutation label for this round is A111C
What was your command line? I suspect that whatever your flags were, it just took the difference of the two best-scoring structures, rather than the paper protocol of the average of the best three.
Hi everyday847,
Thank you for your help. The attachments are my command line and options file. Is there something incorrect if I want to use talaris2013 while keeping other parts the same as the paper protocol?
In addtion, are you sure the ~-1000 score is for talaris2013 in my protocol? The thing is, when I use score_jd2 to score the structure, I only got score of ~-770 and I think talaris2013 is default for score_jd2.
Thank you.
Yours sincerely
Cheng
#main body for the command line:
ddg_monomer.linuxgccrelease @ /home/ucbechz/Scratch/20150203_ddg_monomer_8398mutants/input/options/A111C.options > ddg.log
#options file:
-ddg::mut_file /home/ucbechz/Scratch/20150203_ddg_monomer_8398mutants/input/mutfile/A111C.mutfile
-in:file:s /home/ucbechz/Scratch/20150203_ddg_monomer_8398mutants/input/C226S.pdb
-constraints::cst_file /home/ucbechz/Scratch/20150203_ddg_monomer_8398mutants/input/input.cst
-ddg:weight_file soft_rep_design
-ddg:minimization_scorefunction talaris2013
-ddg::iterations 50
-ddg::dump_pdbs true
-ignore_unrecognized_res
-ddg::local_opt_only false
-ddg::min_cst true
-ddg::suppress_checkpointing true
-in::file::fullatom
-ddg::mean false
-ddg::min true
-ddg::sc_min_only false
-ddg::ramp_repulsive true
-unmute core.optimization.LineMinimizer
-ddg::output_silent true
-override_rsd_type_limit
> Is there something incorrect if I want to use talaris2013 while keeping other parts the same as the paper protocol?
Not necessarily; you'd just asked.
> In addtion, are you sure the ~-1000 score is for talaris2013 in my protocol?
Looking at your ddg log output, I see a ton of lines outputting scores around -1000. I suspect that the score line in your scoring output is similarly the score under talaris. I am not sure what total_score is referring to here or why it differs from score; I would ignore it for now (I'll keep thinking).
Hi everyday847,
Thank you. I look forward to your new thought about the score.
Yours sincerely
Cheng