Msms surface
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Included in psico | |
Module | psico.msms |
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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