# More about Segment ID

**URL:** <https://ask.bioexcel.eu/t/more-about-segment-id/2520>\
**Category:** HADDOCK\
**Created:** [October 21, 2020, 5:03pm UTC](https://ask.bioexcel.eu/t/more-about-segment-id/2520 "2020-10-21T17:03:50Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Santoshs1](https://avatars.discourse-cdn.com/v4/letter/s/e36b37/32.png) [@Santoshs1](https://ask.bioexcel.eu/u/Santoshs1)\
**Post date:** [October 21, 2020, 5:03pm UTC](https://ask.bioexcel.eu/t/more-about-segment-id/2520/1 "2020-10-21T17:03:50Z")

</div>

Hello

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.

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [October 21, 2020, 5:35pm UTC](https://ask.bioexcel.eu/t/more-about-segment-id/2520/2 "2020-10-21T17:35:05Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![Santoshs1](https://avatars.discourse-cdn.com/v4/letter/s/e36b37/32.png) [@Santoshs1](https://ask.bioexcel.eu/u/Santoshs1)\
**Post date:** [October 22, 2020, 5:57pm UTC](https://ask.bioexcel.eu/t/more-about-segment-id/2520/3 "2020-10-22T17:57:40Z")

</div>

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.

---

<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [October 22, 2020, 6:12pm UTC](https://ask.bioexcel.eu/t/more-about-segment-id/2520/4 "2020-10-22T18:12:06Z")

</div>

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