If you load a structure determined by X-ray crystallography, there are often stretches of residues that were not visible in the electron density map, the structure has a gap. Because there is no way to distinguish between a true gap and an unintentional gap created during modeling, YASARA ignores gaps unless they are explicitly marked as true gaps. This can be helpful, as you get for example a continuous ribbon display that bridges gaps, but sometimes it is not what you want. In these cases, just delete all peptide bonds that are longer than 3 Angstroms: Go to Edit > Delete > Bond, click on atom name 'C' in the first window, 'N' in the second window and input 3 A as the minimum bond length required for deletion.

If after deleting the bonds, you save the structure as a PDB file and load it again, all bonds will reappear, because PDB files do not store information about deleted bonds. In such a case, you might consider adding a split point (an explicit chain break) at the position of the gap: Go to Edit > Split > Residue and select the residue after the gap. Split points appear as 'TER' entries in the PDB file and as vertical lines in the sequence selector at the bottom.