Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area?
JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees < [email protected]> wrote: > 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 > -- ******************************************* Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: [email protected] *******************************************
