The question was: "Can anyone tell me if there is a simple way in O to change a proline residue (built using a general model building program) into a cis-proline with standard geometry ? Failing that, is there a utility for doing so around (preferably in the public domain) ?"
Alwyn replied: "Copy the regularization dictionary that you normally use from the odat directory. Use a text editor to locate data for prolines (search for PRO), then move to the line for CA atoms, change the 180 to 0. Use this new dictionary for your next regularization, using a zone of +/- 2 residues on either side of the proline."
ODB file file://rose.bmc.uu.se/pub/gerard/omac/cis_proline.odb contains a macro to change a trans-Pro into a cis-Pro (the nearby main-chain atoms are moved as well). You'll still need to follow Alwyn's hints about Refi-ing afterwards with a modified dictionary, but it should be slightly simpler to actually change the coordinates. (The way it works is as follows: take a Gly-cis-Pro-Gly fragment, lsq-fit it onto the X-Pro-Y of your structure, merge atoms; the N-atom of your residue "X", and the C of "Y", as well as their side chain atoms, are not affected.)
Thilo Stehle added: "You have to call them CPR instead of PRO in your PDB file, and then you can refine them in O to be cis-prolines."