The question: "I tried to use refi to optimize model containing a lot of ssbonds. Half-cystines are named in original PDB-input file CYS. If refi_zone contains cysteines Refi_zone responds like
> undefined atoms in structure : > ires name iatom atom > ires name iatom atom .. > 1 R118 5 SGZ > 1 R118 6 CBZ > 1 R118 7 CAZ > 1 R118 7 CAZ > 1 R118 7 CAZ > Number of cycles is 10 > R.m.s.d. in bond lengths, angles, fixed diherals > 4094.80 2.39 7.31Atoms SGZ, CBZ and CAZ are missing indeed with these names, but present in other CYS. How to make O know that SGZ, CBZ and CAZ are SG, CB and CA in other CYS? O seems not to recognize SSBOND lines."
Alwyn explained: I never got around to tidying this up. the 'strange' atom names are not mapped to the equivalent atoms of the disulphide. This means that the stereochemistry in th elinage is not set up. This gets fixed in refinement. if you do not like the message, call the residue CYH or edit the refi dictionary entry for CYS.