Thursday, September 15, 2016

Installing Latest PyMOL Software for FREE

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Introduction to PyMOL

PyMOL is a Python-enhanced OpenGL based molecular visualization tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is available at SourceForge.net (https://sourceforge.net/projects/pymol/) for free to everyone. The commercial graphical end PyMOL is developed, maintained and distributed by Schrödinger, Inc (https://www.pymol.org/). PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. According to the original author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.

Requirements for PyMOL Installation

In this tutorial, I have explained how to install the latest PyMOL software (the latest version of PyMOL software as on September 15, 2016 is 1.8.3.2) for free. I have chosed Windows 10 Enterprise OEM 64-bit operating system to install the PyMOL software. So, I have downloaded all stable version executables in 64-bit. Before begining to install the PyMOL, we have to download the Python software and needed Python packages with same version. For example, I have chosen Python version 3.x, So I have downloaded the Python packages supporting 3.x version and x64(64-bit).

1. Python v3.5.2 - https://www.python.org/ftp/python/3.5.2/python-3.5.2-amd64.exe (File Size: 28.7 MB)

Download PyMOL and neccessary packages from the unofficial windows binaries portal (http://www.lfd.uci.edu/~gohlke/pythonlibs/)

2. PIP v8.1.2 - http://www.lfd.uci.edu/~gohlke/pythonlibs/dp2ng7en/pip-8.1.2-py2.py3-none-any.whl (File Size: 1.14 MB)

3. Numpy+MKL v1.11.1 - http://www.lfd.uci.edu/~gohlke/pythonlibs/dp2ng7en/numpy-1.11.1+mkl-cp35-cp35m-win_amd64.whl (File Size: 111 MB)

4. PMW v2.0.1 - http://www.lfd.uci.edu/~gohlke/pythonlibs/dp2ng7en/Pmw-2.0.1-py3-none-any.whl (File Size: 533 KB)

5. PyMOL v1.8.3.2 - http://www.lfd.uci.edu/~gohlke/pythonlibs/dp2ng7en/pymol-1.8.3.2-cp35-cp35m-win_amd64.whl (File Size: 7.03 MB)

6. PyMOL Launcher v1.0 - http://www.lfd.uci.edu/~gohlke/pythonlibs/dp2ng7en/pymol_launcher-1.0-cp35-cp35m-win_amd64.whl (File Size: 207 KB)

Total download size of the complete softwares will be around 148.61 MB.

Installation Procedure

1. Install the downloaded Python v3.5.2 sofware with administrator priviliges. Follow the Customize installation procedure as shown in the images below to change the installation directory.
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2. Copy the downloaded Python packages PIP v8.1.2, PMW v2.0.1, PyMOL v1.8.3.2, PyMOL v1.0, PyMOL Launcher v1.0, and Numpy+MKL v1.11.1 to the directory (C:\Python35\Scripts).
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3. Run Command Prompt with administrator priviliges. Enter the command line (cd "C:\Python35\Scripts") to enter into Scripts directory.

4. Enter the following commands in the Commmand Prompt in the order given below to install PyMOL. Refer the snapshot given below for clarification.
  • pip install pip-8.1.2-py2.py3-none-any.whl
  • pip install numpy-1.11.1+mkl-cp35-cp35m-win_amd64.whl
  • pip install Pmw-2.0.1-py3-none-any.whl
  • pip install pymol-1.8.3.2-cp35-cp35m-win_amd64.whl
  • pip install pymol_launcher-1.0-cp35-cp35m-win_amd64.whl
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5. Open the directory (C:\Python35) and double-click the binary file PyMOL.exe to launch PyMOL v1.8.3.2 software.
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11 comments :

  1. Dear Ashok Kumar T.,

    Thank you for this tutorial. I followed your instructions with my own configurations, I used Python 3.6 and cp36 x32 files. I managed to install everything and I can run PyMOL 1.8.6 but I have an issue with the external GUI who doesn't show. I tried to search for an answer to my problem and I think it has something to do with pmg_tk but I don't know anything about Python and I didn't manage to fix my problem.

    Do you have any clue on the way to fix it ?

    Thank you very much for your tutorial,
    Alexis M.

    ReplyDelete
    Replies
    1. Uninstall Python software, clean installed directory, clean registry, etc. Download latest Python software and packages compatible to OS (OS bit, Python version supported packages, etc.). Install software/packages in order as mentioned in the article. Carefully select the check boxes as shown in the figure 1, 2, and 3. before installation.

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  2. Hi, thanks for the tutorial. I have one problem that I think has to do with Windows 10 Enterprise but I am hoping you might be able to help. Everything is running smoothly but if I click using the mouse on either the background or a residue Pymol stalls (Pymol not responding) and the cursor becomes a running circle. After maybe 10-15 seconds the residue is selected and I can work again. If I use commands instead I can select without a stall. Do you have any idea what could be causing this?
    I did have a previous Pymol using Python 27 that has the same problem, which is why I now think it has to do with Windows.
    Thanks very much,
    Klaus

    ReplyDelete
    Replies
    1. I think, the problem is due to slow processor speed.

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  3. That was fast, thanks, however, while it is a laptop it has a i7-3630 QM CPU and when the machine was running Windows 7 it never had this problem. Pymol is the only program I use that has this problem, Illustrator, Photoshop and so on do not have the problem. Any ideas?

    ReplyDelete
    Replies
    1. May be any python class files broken in the modules. Uninstall Python software, clear temp files, cache, broken registry, etc. Download latest Python software and modules accordingly. Check Python software version and OS bit (32/64) while downloading modules (important). Before all, check whether antivirus is protecting your computer properly. If still problem exists, load a small PDB file in PyMol and check it.

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  4. Thanks Prof. Ashok. I reinstalled the lasted version of Python (3.6.2) making sure the versions (amd64) are correct for all the modules. When installing from the cmd line all modules installed correctly (PIP was installed already with the 3.6.2 version). Nevertheless, the problem persists even with a very small pdb file. I am at a university behind a firewall and the antivirus is up to date so I don't believe it is a virus. However, if I am the only person having this problem obviously something is strange with my setup. If you have any other suggestions they would be greatly appreciated, thanks

    ReplyDelete
    Replies
    1. Dear Prof. Klaus Nielsen,
      I'm very sorry to hear this. There is no any other secrets behind the PyMol installation. My suggestions: (i) Update graphics driver and try again, (ii) Run in 'Administrator' mode and try again, (iii) Install in another system and check for same error, and (iv) If you still have same problem, mail to Christoph Gohlke , the real PyMol compiler. Good luck.

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  5. Dear Prof. Ashok,
    Windows had an update this morning and after restarting the PC Pymol now works as it should. Thanks very much for your help.
    Very happy :-)

    ReplyDelete