Reply To: using constraints with AbinitioRelax (Rosetta 3.1)

[Anonymous]

Happy new year!

Thank you for your questions and suggestions. It took me a little while to re-run my test set with __loopfcst:coord_cst_weight __instead of __constraints:cst_weight__, but the RMSD means and variances did not change regardless of the weights that I chose (0, 0.01, 1, 1000). It appears that the constraint file is being read correctly (I can use the __constraints:dmp_cst_set __ feature and get back essentially the same constraint file), but the weights are not being applied, whether they are recognized or not.

Here’s the scorefile with __constraints:cst_weight=1000__

||SCORE: |score |vdw |cenpack |pair |env |cbeta |rg |hs_pair |ss_pair |rsigma |sheet |clashes_total |clashes_bb |description
SCORE: | -7.414 |3.060 |-10.959 |-13.238 |-34.528 |39.187 |46.637 |2.671 |-27.235 |-15.736 |2.726 |0.000 |0.000 |S_00000001
SCORE: |-23.680 |9.892 |-11.907 |-16.523 |-36.105 |36.933 |40.491 |2.738 |-32.290 |-17.254 |0.343 |1.000 |1.000 |S_00000002||

and the output snippet that mentions the constraints:

||core.scoring.constraints: Constraint choice: constraints.dat
core.io.constraints: read constraints from constraints.dat
core.io.constraints: read constraints section –NO_SECTION—
core.io.constraints: no section header [ xxx ] found, try reading line-based format… DON’T MIX
core.io.constraints: read constraints from constraints.dat||

Here’s the scorefile with __loopfcst:coord_cst_weight=1000__

||SCORE: |score |vdw |cenpack |pair |coordinate_constraint |env |cbeta |rg |hs_pair |ss_pair |rsigma |sheet |clashes_total |clashes_bb |description
SCORE: |28078380.206 |2.140 |-12.806 |-19.625 |28078392.256 |-32.807 |40.208 |44.134 |1.862 |-22.495 |-15.386 |2.726 |0.000 |0.000 |S_00000001
SCORE: |39294630.348 |1.758 |-15.278 |-17.152 |39294669.006 |-48.838 |37.422 |40.766 |6.210 |-27.845 |-16.045 |0.343 |0.000 |0.000 |S_00000002||

and the output snippet that mentions the constraints:

||core.scoring.constraints: Constraint choice: constraints.dat
core.io.constraints: read constraints from constraints.dat
core.io.constraints: read constraints section –NO_SECTION—
core.io.constraints: no section header [ xxx ] found, try reading line-based format… DON’T MIX
core.io.constraints: read constraints from constraints.dat||

Clearly the coordinate_constraint term is dominating the score, yet the aggregate results are unchanged. I’m looking more closely at __protocols: :abinitio: :ClassicAbinitio __to understand why, and I have two follow-up questions:

1. How and at what stage are constraints activated in __ClassicAbinitio__? I looked at __rosetta_database/scoring/weights/stageX.wts __but could not find any weights pertaining to constraints.

2. Are the coordinate constraints calculated as a best fit, i.e. automorphic superposition/RMSD? If not, is there a simple way to modify the coordinate constraint class to achieve this? If not, I’ll try to incorporate parts from __core: :scoring: :rms_util__.

Thanks and kind regards,

Nasos