I have problem with pdb file when I want to use for docking becuase they have missing segments and it`s neccessary to minimize energy. I know for Chimera, SwissPDB and Modeller. I want to ask you which is better and how to work with it
You should use either MODELLER or another homology modelling / loop modelling software. Chimera and SwissPDB (Viewer) are visualisation tools and are not suited for this task. The energy minimisation can also be done with MODELLER (if you provide a complete protein and its sequence). Have a look at the manual and/or the tutorial.
To avoid installing and running it locally, you can use the MODELLER interface on the HHpred website.