[Chimera-users] Manually assigning secondary structure to residues

Oren Shalev (Wolfshtat) wolfshta at cs.bgu.ac.il
Thu Aug 16 03:23:49 PDT 2007

Dear Chimera team and users,
I'm modeling chains with gaps using in-house software. When opening in Chimera a model in which a secondary structure element is broken or flanked by the start/end of a gap, the secondary structure of the residue adjacent to the gap is assigned to be 'coil'. I guess this is expected, since one needs to know both Phi and Psi angles to determine the secondary structure of a given residue, yet I always have knowledge that the residue adjacent to the gap does indeed belong to a secondary structure element.
My question is this: is there a way to assign the secondary structure of a given residue to either 'helix' or 'strand'? I'm interested in this for imaging purposes, so potential negative consequences on other aspects of Chimera's operation (perhaps on analysis tools?) don't matter to me.
Thank you,
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