> From: Mirek Cygler [mailto:mirek.cyg...@bri.nrc.ca]
> I wonder if there is a command equivalent to "turn" in > molscript? I would > like to show a cartoon view of my molecule with some > sidechains. When I use > "show cartoon" and include a selection of sidechains, they > appear far from > the backbone worm. Turn off "smooth loops" and "flat sheets" using the cartoon menu or the commands set cartoon_smooth_loops=0 set cartoon_flat_sheets=0 > Can I change the name of the object after loading the > molecule into PyMol? No, but you can create an identical copy and delete the original. load test1.pdb create test2=test1 delete test1 > When I save the molecule can I also save the secondary > structure assignments > with it? I wish...this is on the "to do" list. > Is there a facility within PyMol to detect secondary > structure > automatically? Sort of. util.ss make an attempt at it, but the algorithm in unvalidated (something I just cooked up one morning). For publication, I encourage users to obtain secondary structure assignment via an accepted algorithm. load test1.pdb util.ss test1 show cartoon - Warren
