I have a low-ish resolution (3.5 ) map for a membrane protein. I have been using helical restraints heavily in pymol to do the model building (versions 0.4.2 to 0.5.1 to 0.6 pre release ) . The structure is very homologous to something else and these are really long membrane spanning helices. So a large part of the structure should be helical and thats my justification for using the restraints in coot.
I have mostly refined in refmac ( newest 5.3 ) and some in phenix. Both of these pick the refining restraints automagically. My problem is that my helices look perfect in coot , with the torsions and h-bonding looking pretty good .All the traffic lights ( with and without torsional and ramchandran and helical restraints) are green. But pymol simply refuses to cartoonize my "helices" as helix. I know I can force the pymol cartoon algorithm to treat those regions as helix but am concerned that something is not correct in the way I built my model. Any clues on forcing my helices to conform to what pymols idea of a helix is. The pymol version is also 1.0r2 and does cartoonize everything else as expected. Hari Jayaram
