Hi Faisal, you could run dssp2pdb by James Stroud ( http://www.jamesstroud.com/software/dssp2pdb/ ) to convert dssp output into PDB readable format as part of the header. When you open resultant PDB in PyMOL, secondary structure as defined by dssp would be displayed.
OR one could also define secondary structure in PyMOL manually (see at the end of this link: http://pymol.sourceforge.net/newman/user/S0260cartoons.html) HTH, Partha On Thu, Sep 26, 2013 at 4:02 PM, Faisal Tarique <faisaltari...@gmail.com>wrote: > > Dear all > > Sorry for the off topic question. > > My protein has few G310 helices. It is clearly visible through STRIDE or > DSSP, but when i open the structure in PYMOL it didnt show it. Other > visualization graphics like CHIMERA and VMD are able to pick few of them > but not all the G310 helices..For manuscript preparation i have drawn the > topology diagram taking the output from STRIDE and DSSP while the overall > 3D structure is from PYMOL..Will it be O.K to show some helices missing > from the output of pymol while they are present in the toplogy diagrma ? or > the reviewer will raise the issue? hope you are able to understand what i > mean to say. > > Please suggest me > > -- > Regards > > Faisal > School of Life Sciences > JNU >
