Hi Donghui, Bernhard is correct: PyMOL flattens out secondary structure to produce more aesthetically appealing images. You can disable this for beta sheets and loops by typing:
# disable smoothing of sheets set cartoon_flat_sheets, 0 # disable smoothing of loops set cartoon_smooth_loops, 0 The cartoon_sidechain_helper setting automatically modulates these settings. If for some reason you need to disable cartoon_sidechain_helper you can imitate the look with: hide show cartoon show sticks, not (n. C+CA+O+N) extend 1 set cartoon_smooth_loops, 0 set cartoon_flat_sheets, 0 Again as Bernhard noted, smoothing representations adjusts the representations' positions in space; therefore, you have the option of being positionally correct or aesthetically more pleasing. Cheers, -- Jason On Wed, May 29, 2013 at 10:29 PM, wu donghui <[email protected]> wrote: > Dear all, > > I found a problem when I use pymol to prepare structure interface. Strand > is distorted when residue from the strand is connected to the strand by > turning on "side_chain_helper on". However when side_chain_helper is off, > the strand turns to normal shape but the residue from it is disconnected to > the strand. I attached the picture for your help. I know there must be some > tricks for this. Welcome for any input. Thanks a lot. > > Best, > > Donghui > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) [email protected] (o) +1 (603) 374-7120
