Visualization of docking results

Good Day! There are problem with visualization of protein-protein docking results. Molecule of ligand (small protein - 6 residues) after getting pdb output file with docking results (used HADDOCK webserver 2.2, easy interface. All input files and results of docking process are corrected) are displayed incorrect in:
PyMol - as breaked chain, residues are scattered in space.
Pdb_Viewer from - looking alike in PyMol
Chimera - as stratched chain, which also locate far from docking target.
Could you help me, what the reason and how it may be corrected?
Thank You!

Looks like your molecule is “exploding” - typically caused by bad starting models…

How did you obtain your starting model?

convert 1let sequences in molconvert to mol. Add protection groups in MarvinSketch, convert to pdb in OpenBabel (with option "Generate 3D coordinates’). And starting file of peptide in Pymol and other programs are displayed correctly…

Correct display doesn’t mean the structure is of good quality… And if you add all kind of protection groups, these might simply not be be supported by HADDOCK.

Are you using the web server or a local version?

I’m using web server. Protection groups (Metyl-, and Ac) were added only for C- and N- termial aminoacids

Again - this is a problem of your starting structures and not the docking itself. Did you try simply building your peptide in PyMol for example.

What is the sequence of your peptide?

Can you share your PDB file?

I emailing it to you now


It has a very weird residue numbering with 21 residues defined for what should be only 6!!!

Open the file in a text editor to have a look at it and you will directly see something is wrong.

Try to use PyMol to build the peptide.