Hello, I am doing protein and antibody docking and it seems that the resulting PDB file has a split in that was not exist before the docking. Here I attach the image of the resulting PDB file opened in Pymol. The residues on the edge of the split are subsequent residues (G208 and I209). I use the EASY access and with default parameter. I also has specified the active residues.
What could possibly cause this and is there a way to repair it? Thank you very much in advance.
There is simply a segment missing in your input structure and this is a visualisation (the dashed lines)
Anyway, these long disordered loops can better be removed for the modelling.
Hi there, PyMol represents “disconnected” segments within the same chain with this dotted line if there are no CONNECT records in your structure. Before inputting this structure to HADDOCK, was this region the end of a chain?
But anyways, this is likely a visual representation glitch because the structure outputted by HADDOCK does not contain all the records as the one you inputted - this is not an issue, just may give you this weird representation.
In PyMol you can tweak this visualization, have a look at cartoon_gap_cutoff;
With cartoon_gap_cutoff > 0, if there are missing residues along the protein backbone (e.g. missing loops), PyMOL will create a dashed cartoon loop segment if the gap (in number of residues) is shorter than the cutoff.