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Then I found that the '3ZEX.pdb' file contains totally 4200 nucleotides, while the '3ZEX.dssr' file concerns only 4177 nucleotides.It'd have been helpful if you were specific as to which nts are not recognized by DSSR. Checking the PDB entry 3zex (http://www.rcsb.org/pdb/explore/explore.do?structureId=3zex), I found that this structure was solved by electron microscopy at a resolution of 5.57 Å. At such a lousy resolution, it is expected to see local distortions so that some nts are beyond 'recognition' (by default). One example is shown below, for A.G162: see how far off the six-membered ring is from the five-membered ring. Other 'missing' nts may well be due to similar reasons.
Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.