After the 1.2065 production release, a bug crept into the code that determines secondary structure when HELIX and SHEET records are absent.  I'm guessing your structure is lacking these records and therefore the helices aren't being properly identified.  You can manually identify them to Chimera by using the procedure Elaine outlined, quoted below.

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        pett@cgl.ucsf.edu

                        http://www.cgl.ucsf.edu


On Aug 30, 2005, at 11:21 AM, Elaine Meng wrote:

You can change assignments

     (a) manually (by selecting the desired parts, then clicking the button

reporting what is selected on the bottom right corner of the Chimera window

to open the Selection Inspector, Inspect "Residue" instead of "Atom," setting

"in helix" to "true" and "in strand" to "false")