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PHENIX programs in Scipion. Warning: Install PHENIX v. 1-17

Project description

Phenix scipion plugin

This plugin allows to use programs from the PHENIX software suite within the Scipion framework. You need to install the Phenix suite before installing the plugin, see section “Binary Files” for details.

Phenix is a software suite that allows model building of macromolecule structures obtained by X-ray crystallography, and that has been extended to other techniques like cryo-EM (see Phenix home page for details).

Current programs implemented:

  • dock in map

  • emringer

  • real space refine

  • molprobity

  • superpose pdbs

  • validation cryoem

Install this plugin

You will need to use 3.0.0 version of Scipion to run these protocols. To install the plugin, you have two options:

  • Stable version

scipion installp -p scipion-em-phenix

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-phenix.git
  1. Install:

scipion installp -p path_to_scipion-em-phenix --devel
  • Binary files

PHENIX binaries will NOT be installed automatically with the plugin. The independent installation of PHENIX software suite by the user is required before running the programs. Default installation path assumed is /usr/local/phenix-1.13-2998; this path or any other of your preference has to be set in PHENIX_HOME in scipion.conf file. We recommend to install PHENIX version 1.13-2998.

the plug-in also requires imagemagick package: sudo apt-get install imagemagick

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

scipion-em-phenix-3.0.2.tar.gz (137.6 kB view hashes)

Uploaded Source

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