More about Segment ID


I am finding HADDOCK very useful to dock two proteins based on XL-MS restraints.

I am unable to understand what segment ID is.

Please enlighten me.

Thank you very much.

It is the equivalent of the chain ID (but formally written at a different location in the PDB file).

I am creating the PDB file by using the “Export Molecule” option in PyMOL.

Here I specify that segment identifier should not be written. Hence I am sure that PDB files that I input for HADDOCK do not have segment identifier columns.

I am trying to dock two protein molecules based on distance restrains obtained from XL-MS.

Molecule 1 has a chain labelled A and Molecule 2 has a chain labelled C.

So, even if my PDB files have no segment identifier columns, should I still specify the segment identifier for Molecule 2 as C? Please help me here.

Based on the naming of the chains in the two molecules, the tbl file restraints has the following syntax:

assign (segid A and resid 1 and name CA) (segid C and resid 1 and name CA) 20.4 20.4 0

Can you please tell me if this is alright or if I need to correct anything.

Thank you very much.

If you don’t specify segment ID in the server forms, the default will be:

molecule 1 -> A
molecule 2 -> B
molecule 3 -> C

I.e. it is not extracting the segmend/chainID from the input PDB file.

And your restraint example will thus not work since you expect C but you only have A and B (unless you explicitly assign in the server input forms A and C