Haddock3. Module [caprieval] without refference structure

HADDOCK
1

Hi.
How I can to use module [caprieval] without reference structure?
Could you please show me an example of code for .cfg file for using “best scoring model” as a reference?

Thank you

2

Hi,

simply do not specify any reference_fname file:

[rigidbody]
tolerance = 5
ambig_fname = “data/ambig.tbl”
sampling = 3000

[caprieval]

[seletop]

3

Simply add it to the workflow without defining any reference. It will automatically use the best model

4

Thank you I will try it. It’s very helpful

5

After running job with [seletop], instead reference structure. It was running all modules without crushing. But in log file I got Warnings. I afraid it’s did not work well.

[capri WARNING] No reference interface found
[capri WARNING] Not enough chains for calculating lrmsd
[capri WARNING] Not enough chains for calculating ilrmsd
[capri WARNING] No reference contacts found

Haddock didn’t calculated any statistics, only score.
Does it supposed to be like this?
Maybe someone have any ideas what could be wrong?

6

Warnings are ok.

But the warnings below indicate that you must have only one chain in your system.
Therefore the docking metrics can not be calculated.

What is the system you are modelling?

7

I’m modeling antibody-antigen, I believe in tutorial was indication to renumber and rename chains in an antibody. I have chain A for antibody (instead of H and L), with unique renumbered residues. In antigen I have chain B. IS problem with renamed antibody in this case? Maybe it will be helpful for others

8

Indeed, as stated in the tutorial, it is easier for haddock to treat the antibody as a single chain, otherwise you would have to go for a three-body-docking and generate restraints for the two chains of the antibody.

There have never been any problem regarding renaming the antibody as a single chain, as long as residue numbers are all different.

9

Thank you so much for trying to help me with this! It really helped me spot my mistake, so I’m super grateful. I’m really sorry about the confusion. I had an antibody with one chain labeled A, but somehow the antigen chain didn’t get renamed and was also labeled A. That’s why Haddock3 couldn’t run the docking. But no worries now—everything is sorted out! I fixed the code using pdb-tools and renamed the antigen chain to B. Thanks a ton for your help, and I apologize for any inconvenience.

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10

Glad you made it !
No apologies needed, this forum is made for this.

1 Like