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A Scipion plugin to manipulate atomic structure files (PDB/MMCIF)

Project description

Atom_struct_utils scipion plugin

Utilities for handling PDB/mmcif atomic structure files:

Current plugin protocols:

  • operate (option extract): extract a chain from an atom structure (pdb/cif file).
  • operate (option add): perform union of several atomic structures.
  • convert_sym: takes an atomStruct in any icosahedric symemtry and rotates it to another.

Install this plugin

You will need to use 2.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

  • Stable version
scipion installp -p scipion-em-atom_struct_utils


  • through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
  • Developer’s version
  1. Download repository:
git clone
  1. Install:
scipion installp -p path_to_scipion-em-atom_struct_utils --devel
  • Binary files

Atom_struct_utils plugin is a pure Python module, no binary files are required.

  • Tests
To check the installation, simply run the following Scipion test:
  • scipion test –grep TestOperate –run
  • scipion test –grep TestConvertSymmetry –run

Buildbot status

Status devel version:

Status production version:

Project details

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Files for scipion-em-atomstructutils, version 2.0.3
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