Write modeller scripts in MAC

MODELLER is a software used for homology or comparative modeling of protein three-dimensional structures,  The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. so we have to add Hydrogen atoms after calculate our modell. Following tutorial is easy to create and install modeller, sometimes is necesary to download Python package and we need a compiler to install packages easily for this reason we need to intall X code our use another compiler. 

To download modeller just click in the link: Modeller

Note: cd command will allow you to change directories. When you open a terminal you will be in your home directory. 

To run modeller open terminal:

Once installed the package of modeller access through terminal whit the comand cd if your folder of scripts is in desk example tipe:

  

$ cd Desktop

then you will be in the folder Desktop after this access to your folder 

$ cd Proteinx

as an example this is my terminal line

macbook-de-fixxer-2:~ javier$ cd Desktop

macbook-de-fixxer-2:Desktop javier$ cd cryo-em

once you are in the rigth folder to run modeller comands use the comand mod9.9 to call the enviroment of modeller:

macbook-de-fixxer-2:cryo-em javier$ mod9.9

and after the comand to call modeller pack write the script you wan to run example:



macbook-de-fixxer-2:cryo-em javier$ mod9.9 build_profile.py