PCS tensor calc with HADDOCK

HADDOCK
1

Dear all,

I am trying to dock two proteins using a combination of PCS and chemical shift perturbations. I have intramolecular PCS from the protein that the lanthanide is bound to and intermolecular PCS from the protein that I am trying to dock. My understanding is that the initial tensor is calculated from all the pcs that I give as input (using the starting R and D that I input calculated from intra-PCS) and then optimized during the steps of docking. Is there a way to have the tensor set up and optimization only use PCS intra and link the intermolecular values to this tensor? Any help would be greatly appreciated.

Thank you,
Taylor

2

Hi Taylor

I don’t think this is possible on the server. The first step optimises the tensor position / orientation while keeping the proteins fixed in space.

It would require some changes in the scripts to enable such a feature. Doable, but for another version.
Will make a note of it.

Did you define a 0 length distance restraints (as unambiguous) between your lanthanide ion and the tensor? You need that to maintain it at the right location. We support up to 10 PCS restraint set, each in principle with its own tensor (or you can define them to the same tensors).

The tensors will have residue number 999 to 990. And here would be an example of a distance restraint file to a specific residue:

assi (resid  998 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0
assi (resid  997 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0
assi (resid  996 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0
assi (resid  995 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0
assi (resid  994 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0
assi (resid  993 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0
assi (resid  992 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0
assi (resid  991 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0
assi (resid  990 and resn XAN and name  OO ) (resid 190 and segid A ) 0.0 0.0 0.0

This assumes that resid 190 consists of a single atom. Note that if you were to define the ion atom name, make sure to put it between double quote otherwise the restraint will not be used. E.g. "CA+2"