Usage of cross-link MS-derived distance constraints in HADDOCK 3.0

[VGPReys]

Hi DiT,

@DiT

My question is, rigidbody, flexref, and emref modules from the workflow all have “distance restraints“ option. Should I supply my file to all of them or just to the first rigid body module would suffice?

Yes, for each of these modules, you need to supply the restraints files (ambig and unambig) of interest, as you already did

@DiT

My second question is, in previous HADDOCK 2.4 setting, it is recommended to set the “Number of rigid body docking,” “Number of structures for semi-flexible refinement,” and “Number of structures for water refinement” to 10000, 200, 200 respectively. What is the corresponding option in the current HADDOCK 3, or do I need to add the “seletop” module in between modules for the current workflow?

• Yes, to go from 10000 rigidbody docking complexes to 200, you should use the “seletop” module, with the parameter “select = 200”.
• I would place it between the rigidbody and flexref modules, instead of doing a clustering (clustfcc - seletopclusts).
• I would place the clustering step only after the emref module, as you already did.
• I would not terminate the workflow by seletop