My helices look like corkscrews (and/or my beta sheets look like tubes) Whats wrong?
Your PDB file lacks HELIX and SHEET records describing where secondary structure exists. Ribbonjr doesn’t determine the position of secondary structure motifs; it relies on these records. You don’t have to create them by hand though; check the ksdssp command in the manual. From within Midas it can be used to add HELIX and SHEET information to the open model(s). From the UNIX command line (see Appendix 6) it can be used to create a file of HELIX and SHEET records which can be added to your PDB file permanently.
