Hi Francesco,

Segment ID is no longer a supported field in the PDB format.  This is likely why Chimera isn't preserving your segment information.  Nonetheless, the columns where segment ID used to be defined (in earlier versions of PDB) have nothing defined for them in the current PDB version.  Also, the low-level PDB read/write routines in Chimera have support for segment ID columns but the upper layers do nothing with that support.  So I see no reason why we couldn't add seg-ID-preservation to Chimera.  Though it shouldn't be too hard to do I nonetheless have quite a few projects on my hands right now, so it may be weeks or months before I'm able to get to it.  I will open a feature-request ticket for it in our bug database and put you on the recipient list so that you'll be notified when it gets implemented.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        http://www.cgl.ucsf.edu