when i am open my protein(eg-1cqe) in swiiss pdb viewer ,it show some aminoacids side chains are missing..why?1cqe is a complete reference protein.
Not sure what you mean by "complete reference protein" - presumably you mean that a corresponding sequence record (e.g. in UniProt) is annotated as "complete"?
However: to expand on the comment by dpryan79. It is not uncommon for residues to be missing from protein structures. This happens when regions of protein molecules in the protein crystal are disordered, mobile or "floppy" and so do not generate an interpretable X-ray diffraction pattern.
Here is an introduction to protein crystallography which explains this and other issues; there are many others on the Web.
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version 2.3.6
Maybe parts are flopping around. You won't see them in a structure then.
You'll get better answers if you use more informative question titles and tags. In this case: "why are residues missing in this protein structure?" and "protein, crystallography, structure" would be good. Fixing that for you now...
Are you sure that the amino acids are in the pdb file?
The original question could have been rephrased as why not all residues in a protein were contained in its structure, so no, they weren't in the structure. See my comment above and Nielfws' reply below.