Msms surface

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Included in psico
This command or function is available from psico, which is a PyMOL extension.

Module psico.msms

msms_surface calculates a molecular surface with MSMS and loads it into PyMOL as a CGO.

Installation

msms_surface is available from the psico package and requires the msms binary.

All dependencies are available from Anaconda Cloud:

conda install -c schrodinger pymol
conda install -c schrodinger pymol-psico
conda install -c bioconda -c speleo3 msms

Usage

msms_surface [ selection [, state [, density [, name
    [, atomcolors [, exe [, preserve ]]]]]]]

Arguments

  • selection = str: atom selection {default: polymer}
  • state = int: object state {default: 1}
  • density = float: MSMS surface point density {default: 3}
  • name = str: name of CGO object to create
  • atomcolors = 0/1: color surface by atom colors {default: 0}
  • exe = str: path to msms binary {default: find in $PATH}
  • preserve = 0/1: don't delete msms generated files {default: 0}

Examples

Use atom colors:

import psico.msms
fetch 1ubq, async=0
msms_surface atomcolors=1

Use a solid color:

msms_surface name=bluesurf
color blue, bluesurf

See Also