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
Download repository:
git clone https://github.com/scipion-em/scipion-em-phenix.git
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
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