Hi Jacob, Sure, but I believe Donghui wanted to only show sidechains, not any backbone atoms, as sticks. Doing this will leave fragments floating in space as the original email noted.
Cheers, -- Jason On Thu, May 30, 2013 at 10:13 AM, Jacob Keller < [email protected]> wrote: > > 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] > > ******************************************* > -- Jason Vertrees, PhD Director of Core Modeling Products Schrödinger, Inc. (e) [email protected] (o) +1 (603) 374-7120
