DSSP & Stride Plugin for PyMOL

Introduction

The DSSP & Stride Plugin for PyMOL provides a graphical user interface for coloring proteins according to the secondary structures assigned by DSSP or Stride in PyMOL.

Created by Hongbo Zhu <hongbo.zhu.cn @ googlemail>, Biotechnology Center (BIOTEC), TU Dresden. Please cite this plugin if you use it in a publication.
1. Citation for this plugin:
    Hongbo Zhu.
DSSP & Stride plugin for PyMOL, 2011, Biotechnology Center (BIOTEC), TU Dresden.
2. Citation for PyMOL can be found at: http://pymol.sourceforge.net/faq.html#CITE

Installation

1. Obtain a copy of DSSP binary and/or Stride binary (You can use either program or both programs. DSSP and Stride are not included in the plugin).
2. (optional) set environmental variables DSSP_BIN and STRIDE_BIN to the dssp and stride executable.
3. Download dssp_stride_pymol.py.
4. In PyMOL, go to Menu → Plugin → Manage Plugins → Install... and install dssp_stride_pymol.py. Restart PyMOL.

Usage

After execute "Run DSSP" or "Run Stride", several (<=8) selections will be generated. The names of selections are of the format “yousele_H_prog_1234” (see Figure 3). The first part is the input selection name, the second part is one of the SSEs used in DSSP (HGIEBTS-) or Stride (HGIEBbTC), the third part is the program name (DSSP or Stride), and the third part is a 4-digit random number.

Update Color” will color the input selection using the color scheme defined in the “Color” tab.

Update ss” will update the input selection using the secondary structures assigned by DSSP/Stride and display the selection in cartoon.

Screenshots



Figure 1: Tab Structure: Specifying structure (PyMOL selection) and DSSP binary.


Figure 2: Tab Color Configuration: Configuring colors for SSEs.


Figure 3: Demonstation of the DSSP plugin (PDB: 1pyg).


Figure 4: Demonstation of the DSSP & Stride plugin (PDB: 1pyg).
 

If you have any problem or suggestion about the plugin, please contact Hongbo Zhu <hongbo.zhu.cn @ googlemail>.

Last update: 2011 Apr. 28.