RosettaCM: adding constraints while keeping AUTO constraints

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RosettaCM: adding constraints while keeping AUTO constraints
#1

Hi all,

I am working on the structural prediction of a symmetric multidomain protein using RosettaCM - I have to add a tetramerization domain for which no template structure is available, but for which I can set some distance constraints to steer the prediction in the right direction. For this, I changed

    <MOVERS>
<Hybridize ...>
<Fragments .../>
<Template pdb="xxx.pdb" cst_file="AUTO" weight="1.000" symmdef="xxx.symm" />
</Hybridize>
</MOVERS>

to

    <MOVERS>
<Hybridize ...>
<Fragments .../>
<Template pdb="xxx.pdb" cst_file="xxx.cst" weight="1.000" symmdef="xxx.symm" />
</Hybridize>
</MOVERS>

where xxx.cst only contains 4 manually defined harmonic constraints. The structures of the added domain look very promising, but the coordinates of the rest of the protein deviate a lot from the template structure, which is not the case if I set cst_file="AUTO" (but then, the added domain is not folding correctly). I suppose that this is caused by omitting the "AUTO" constraints.

Is there a straightforward way to combine the manually defined constraints with the "AUTO" constraints? Maybe via the input options? Or is there a way to write out the "AUTO" constraints as a file? I seem to be missing something very obvious, but I can't put my finger on what it is.

Michele

Post Situation:
Sun, 2020-08-30 10:42
Michele.Bonus

Hello,

unfortunately there is no way to do this currently without doing some c++ coding.

check out the "generate_centroid_constraints" function in src/protocols/hybridization/util.cc

you will want to remove the call to pose.remove_constraints()

you will also want to set:

keep_pose_constraint="1" in the hybridize setting, and you should add the constraints before hybridize using the ConstraintSetMover

hopefully that sets you on the right path!

Sun, 2020-08-30 22:18
danpf

Thanks for the reply! I'll give it a try (or two .. I'm very shy about C++ code) and keep you updated.

Would there be a way to include this feature in a future weekly release; that is, combining AUTO with constraints from a cst_file? I can think of a variety of applications where this could be useful for the broader audience.

Sun, 2020-08-30 23:06
Michele.Bonus