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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
  1. Download repository:
git clone https://github.com/scipion-em/scipion-em-atom_struct_utils.git
  1. 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 flex   (command valid for ubuntu/debian and similar OS)
sudo apt install tcsh   (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

See Model Building Tutorial

Problem compiling maxit?

Try:
  • install bison, flex, csh, tcsh
  • edit the file ./cifparse-obj-v7.0/Makefile (in scipion/software/em/maxit-version) and replace "mv" by "cp"

Buildbot status

Status devel version:

Status production version: