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Instructions for Installing PyRosetta on Windows 10


Instructions for Installing PyRosetta on Windows 10 with Anniversary Update

Page created 10/2016 using Windows 10 Home, version 1607

This article is intended to guide a user through the process of updating Windows 10 with the Anniversary Update, enabling BASH, and installing PyRosetta.  The process will require at least one reboot of the computer.  If the Anniversary Update is not installed, plan for a longer window of time, in order to install the update.  If it is already installed, skip to step 2.


Installing BASH

Windows update

Make sure Windows is up to date on your computer.

    a.      Open Settings.  This can be done by clicking the gear symbol in the bottom left when you tap the Windows key or click the bottom left icon.  Alternatively, you can type ‘Settings’ into the search.



    b. Go to Update & Security

    c.       Select the Windows Update tab on the left sidebar

    d.      Select Check for updates


    e.      If the Anniversary Update has not been installed, there will be updates listed to install.  Install them. This may require some time and several reboots.
 

Change to Developer mode

Windows must be in Developer mode to use BASH.

    a.       Again under Settings, go to Update & Security (see above)
    
    b.      Select the For developers tab on the left sidebar
    
    c.       Select Developer mode 
 


Activating Linux

    a.       Open the Control Panel.  This can be done with a search, or by scrolling down the apps list to Windows System > Control Panel 
  

    b.       Go to Programs 
    

    c.       Go to Programs and Features 
  

    d.      Go to Turn Windows features on or off, on the left sidebar
  

    e.      Check the box for Windows Subsystem for Linux.  Note: This option is not available if the Anniversary Update has not been installed. 
  

    f.      At this point, one needs to open the Windows store and install one of the Linux flavors.  Go to https://aka.ms/wslstore, choose Ubuntu, install.  Then open bash.  Then it forces you to make a new user with a password.  Implementing this change will require a reboot of your computer.


Accessing BASH

After the restart, BASH should be available.  It can be accessed either with a search or by scrolling down the apps list to Bash on Ubuntu on Windows.  There are several install options.


Option 1: Set up a BASH user account

This approach is safer, but will require the use of that password and ‘sudo’ for subsequent steps.  It reduces the risk of a casual user accidentally messing things up.

Open a BASH window and create a username and password. 

Option 2: Set up a root account

With this approach, you are always the super user, so ‘sudo’ and a password input will not be necessary when using BASH from this account.

Open a Windows terminal (not BASH).  A terminal can be opened either with a search, or by scrolling down the apps list to Windows System > Command Prompt 


           In the terminal window, enter the following:
                             
    lxrun /install /y

 

Installing and running PyRosetta

Installing BASH functions

The following functions will be needed to properly set up PyRosetta4
Open a BASH window (see above) and type the following commands. Note that the 'sudo' may be omitted if the second BASH installation option was chosen. Otherwise, the first 'sudo' command will prompt you to put in the password you created.
sudo apt-get update
sudo apt-get install ipython
sudo apt-get install python-setuptools


Download PyRosetta

There are several options for this.  In either case, you should make or choose a directory for PyRosetta.  

Option 1: Installing by direct download

Preferred method

    A.  Go to the PyRosetta 4 downloads page.

    B.  Enter username and password

    C.  Download the appropriate Linux Release, based on your Python version 

    D.  Move the downloaded file to the desired directory.  

    E.  In BASH, move to the PyRosetta directory
cd [your PyRosetta directory, ex: /mnt/c/Users/jhlubin/PyRosetta/]

    F.  Unpack PyRosetta
tar -vjxf [PyRosetta file, ex: PyRosetta4.Release.python27.linux.master-58947.tar.bz2]


Option 2: Installing using git

More applicable for users planning to modify Rosetta

    A.  In BASH, enter the following command to install Git:

sudo apt-get install git

    B.  In BASH, move to the PyRosetta directory

cd [your PyRosetta directory, ex: /mnt/c/Users/jhlubin/PyRosetta/]

    C.  Enter the following commands to download PyRosetta

git init
git clone http://[USERNAME@]graylab.jhu.edu/download/PyRosetta4/git/release/PyRosetta4.MinSizeRel.python27.linux.release.git/

    D. Enter password

    There may be a long delay without any message displaying in the terminal while the file copies into your directory. This is due to the large size of the file.


Setting up and testing Pyrosetta


Congratulations, you now have PyRosetta! You can set it up with the following commands:
cd [new PyRosetta folder]/setup
This moves you to the setup folder.
sudo python setup.py install
(Note that this requires the Python Setuptools which you installed with an apt-get command earlier.)

You can test PyRosetta with the following commands:
cd ..
This moves you back up from the setup folder to the main PyRosetta4 directory.
python self-test.py

All tests except 'C001_Carbohydrates_Demo01' are expected to pass at this time.


For further testing, try opening an interactive PyRosetta session yourself.  The following commands are a simple example, and their expected output is shown below.  We encourage you to play with PyRosetta further, and to try out the tutorials here.
ipython
Python 2.7.6 (default, Jun 22 2015, 17:58:13)
Type "copyright", "credits" or "license" for more information.

IPython 1.2.1 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.
from rosetta import * 
from pyrosetta import * 
init()
Found rosetta database at: /usr/local/lib/python2.7/dist-packages/pyrosetta-4.0-py2.7.egg/database; using it....
PyRosetta-4 2016 [Rosetta 2016 unknown:0ca4248d244ad1929a9b195d6730421130a12652 2016-09-10 12:27:39 -0500] retrieved from: git@github.com:RosettaCommons/main.git
(C) Copyright Rosetta Commons Member Institutions.
Created in JHU by Sergey Lyskov and PyRosetta Team.

core.init: Rosetta version  from
core.init: command: PyRosetta -ex1 -ex2aro -database /usr/local/lib/python2.7/dist-packages/pyrosetta-4.0-py2.7.egg/database
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-858825760 seed_offset=0 real_seed=-858825760
core.init.random: RandomGenerator:init: Normal mode, seed=-858825760 RG_type=mt19937
p=pose_from_sequence("ACDEFGHIKLMNPQRSTVWY")
print p
PDB file name: ACDEFGHI
Total residues:20
Sequence: ACDEFGHIKLMNPQRSTVWY
Fold tree:
FOLD_TREE  EDGE 1 20 -1
print p.residue(4)
Residue 4: GLU (GLU, E):
Base: GLU
 Properties: POLYMER PROTEIN CANONICAL_AA SC_ORBITALS POLAR CHARGED NEGATIVE_CHARGE METALBINDING ALPHA_AA L_AA
 Variant types:
 Main-chain atoms:  N    CA   C
 Backbone atoms:    N    CA   C    O    H    HA
 Side-chain atoms:  CB   CG   CD   OE1  OE2 1HB  2HB  1HG  2HG
Atom Coordinates:
   N  : 9.53449, 5.35894, 5.86727e-16
   CA : 10.1896, 6.66148, -2.44225e-17
   C  : 11.7058, 6.51548, 9.3584e-16
   O  : 12.2319, 5.40254, 2.76825e-07
   CB : 9.74645, 7.48145, 1.21373
   CG : 8.75059, 6.7733, 2.12125
   CD : 8.39724, 5.39412, 1.63846
   OE1: 8.91075, 4.9912, 0.622485
   OE2: 7.61256, 4.74245, 2.28668
   H  : 10.1015, 4.5231, 1.53279e-15
   HA : 9.89999, 7.19446, -0.906235
  1HB : 10.6181, 7.74355, 1.81372
  2HB : 9.28915, 8.41188, 0.876963
  1HG : 9.17642, 6.69754, 3.12143
  2HG : 7.84419, 7.37357, 2.1867

Note that when you are done with ipython, you can exit the session and return to where you left off in BASH by typing control + d and entering y.


Running the PyMol Mover

For instructions on installing PyMOL, see https://www.pymol.org/install

For tips using the PyMOL_Mover, see http://www.pyrosetta.org/pymol_mover-tutorial

Ideally, having PyMOL and PyRosetta installed, and running PyMOLPyRosettaServer.py in PyMOL should work properly.  However, there are several issues that have been noted, and their solutions follow.

PyMOLPyRosettaServer.py missing 

If PyMOLPyRosettaServer.py is not present in the PyRosetta 4 download, it can be copied and pasted from an older PyRosetta 3 installation.


Port listing issues 

On some computers, the default port for the PyMOL_Mover, 65000, is used by other programs.  (DropBox and NVidia stream service have been identified so far.)  In this case, PyMOL will return something like the following when told to run PyMOLPyRosettaServer.py, and it will be necessary to change the port usage.

PyMOL <---> PyRosetta link started!

at 127.0.0.1 port 65000

Exception in thread Thread-5:

Traceback (most recent call last):

  File "C:\Program Files\PyMOL\PyMOL\py27\lib\threading.py", line 810, in __bootstrap_inner

    self.run()

  File "C:\Program Files\PyMOL\PyMOL\py27\lib\threading.py", line 763, in run

    self.__target(*self.__args, **self.__kwargs)

  File "PyMOLPyRosettaServer.py", line 1141, in main

    udp_serv = PR_UDPServer(ip, port)

  File "PyMOLPyRosettaServer.py", line 247, in __init__

    raise StartUpError()

StartUpError: FAILED TO START PyRosetta-PyMOL server.

Do you already have another instance of it running?


a.       To see what ports are in use, open the Resource Monitor.  This can be done with a search, or by scrolling down the apps list to Windows Administrative Tools > Resource Monitor


b.      Go to the Network tab and open the Listening Ports dropdown.  The used ports will all be listed in the Port column.


c.       Select a port number that is not in use.  This can be any number between 1024 and 65536.  In the above example, 65002 was used.


d.      Open PyMOLPyRosettaServer.py in a text editor.


e.      Find the line, usually 1186 near the end of the file, that says

 start_rosetta_server('127.0.0.1', 65000)

Change the port from 65000 to the new port number

 

f.        In the future, when running PyRosetta and initiating the PyMOL_Mover, instead of using the command

pmm = PyMOL_Mover()

                                use the following

                                           

pmm = PyMOL_Mover('127.0.0.1', port=[new port number, ex: 65002])

g.       If desired, this change can be made to the following files in the PyRosetta 4 test folder to view  the tests in PyMOL:

·         C001_Carbohydrates_Demo01.py

·         Workshop3test.py

·         Workshop4test.py

·         Workshop5test.py

·         Workshop8test.py

All tests except 'C001_Carbohydrates_Demo01' should pass.


Tips and suggestions

Copying and Pasting in BASH on Windows

You may have noted that control + shift + c and control + shift + v do not work in the Windows BASH as they do on Linux.  The best solution we have found so far is to do the following:
  1. Right click on the top of the BASH window and select Properties

  2. In the dialog box, check Quick Edit Mode. You may also want to Enable Ctrl key shortcuts.  Then press OK.

Now, copying and pasting is possible.  To copy text from the BASH window, highlight it and right click.  Pasting can be done similarly; if you have copied text from elsewhere, right clicking into the command line will past the text into the BASH terminal.

Alternatively, copying and pasting can be made by right clicking the BASH icon and going to Edit.




We hope you have found this guide helpful.
For further questions, we encourage you to go to https://www.rosettacommons.org/forum
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