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
READ The “Binary file” section before installing this package
You will need to use 3.0.0 version of Scipion to run these protocols.
Stable version
scipion installp -p scipion-em-atom_struct_utils
OR
through the plugin manager GUI by launching Scipion and following Configuration >> Plugins
Developer’s version
Download repository:
git clone https://github.com/scipion-em/scipion-em-atom_struct_utils.git
Install:
scipion installp -p path_to_scipion-em-atom_struct_utils --devel
Binary files
Atom_struct_utils plugin is a pure Python module but uses the program “maxit” for conversion of pdb/cif files with atomic coordinates. If not available maxit will be instaled. Prerequisites for maxit are bison, flex, csh and tcsh
sudo apt install bison (command valid for ubuntu/debian and similar OS)
sudo apt install felx (command valid for ubuntu/debian and similar OS)
sudo apt install csh (command valid for ubuntu/debian and similar OS)
Tests
- To check the installation, simply run the following Scipion test:
scipion test –grep TestOperate –run
scipion test –grep TestConvertSymmetry –run
Examples
Buildbot status
Status devel version:
Status production version:
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Source Distribution
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Hashes for scipion-em-atomstructutils-3.0.3.tar.gz
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Hashes for scipion_em_atomstructutils-3.0.3-py3-none-any.whl
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