Installing Latest PyMOL Software for FREE

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PyMOL

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 Python extension packages from the unofficial windows binaries portal of Christoph Gohlke, Laboratory for Fluorescence Dynamics, University of California, Irvine.

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)

 Latest file (for Python v3.5.2, 64-bit): PIP v20.0.2 -
https://download.lfd.uci.edu/pythonlibs/x2tqcw5k/cp27/pip-20.0.2-py2.py3-none-any.whl

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)

 Latest file (for Python v3.5.2, 64-bit): Numpy+MKL v1.16.6 -
https://download.lfd.uci.edu/pythonlibs/x2tqcw5k/cp35/numpy-1.16.6+mkl-cp35-cp35m-win_amd64.whl

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)

 Latest file (for Python v3.5.2, 64-bit): PMW v2.0.1 -
https://download.lfd.uci.edu/pythonlibs/x2tqcw5k/Pmw-2.0.1-py3-none-any.whl

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)

 Latest file (for Python v3.5.2, 64-bit): PyMOL v2.3.0 -
https://download.lfd.uci.edu/pythonlibs/x2tqcw5k/cp35/pymol-2.3.0-cp35-cp35m-win_amd64.whl

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)

 Latest file (for Python v3.5.2, 64-bit): PyMOL Launcher v2.1 -
https://download.lfd.uci.edu/pythonlibs/x2tqcw5k/cp35/pymol_launcher-2.1-cp35-cp35m-win_amd64.whl

Total file size for download of the complete software and packages 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.

PyMOL Setup

PyMOL Setup Optional Features

PyMOL Setup Advanced Options

PyMOL Setup Progress

2. Copy the downloaded Python packages PIP v8.1.2, PMW v2.0.1, PyMOL v1.8.3.2, PyMOL Launcher v1.0, and Numpy+MKL v1.11.1 to the directory (C:\Python35\Scripts).

PyMOL Scripts Directory

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

PyMOL Package Installation

5. Open the directory (C:\Python35) and double-click the binary file PyMOL.exe to launch PyMOL v1.8.3.2 software.

PyMOL Software Directory

NOTE
The pre-compiled windows binaries for Python extension packages are hosted and regularly updated by Christoph Gohlke of the Laboratory for Fluorescence Dynamics, University of California, Irvine, in the source-code repository. Moreover, the links to old windows binaries are removed from the server on the new release of Python extension packages. So, carefully download the apt windows binaries and Python software according to the latest release. As on 24 April 2021, the latest Python software and pre-compiled windows binaries for installing PyMOL are bellow,

1. Python 3.9.4 (https://www.python.org/ftp/python/3.9.4/python-3.9.4-amd64.exe)
2. PIP v21.0.1 (https://download.lfd.uci.edu/pythonlibs/w4tscw6k/pip-21.0.1-py3-none-any.whl)
3. Numpy+MKL v1.20.2 (https://download.lfd.uci.edu/pythonlibs/w4tscw6k/numpy-1.20.2+mkl-cp39-cp39-win_amd64.whl)
4. PMW v2.0.1 (https://download.lfd.uci.edu/pythonlibs/w4tscw6k/Pmw-2.0.1-py3-none-any.whl)
5. PyMOL v2.5.0 alpha (https://download.lfd.uci.edu/pythonlibs/w4tscw6k/pymol-2.5.0a0-cp39-cp39-win_amd64.whl)
6. PyMOL Launcher v2.1 (https://download.lfd.uci.edu/pythonlibs/w4tscw6k/pymol_launcher-2.1-cp39-cp39-win_amd64.whl)


Comments

  1. UnknownJune 13, 2017 at 4:55 PM

    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. UnknownJune 13, 2017 at 5:17 PM

      Also I'm on Windows 8.1.

      Delete
    2. Prof. Dr. T. Ashok KumarJune 14, 2017 at 11:18 AM

      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.

      Delete
  2. UnknownAugust 8, 2017 at 8:34 PM

    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
  3. UnknownAugust 8, 2017 at 9:00 PM

    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. Prof. Dr. T. Ashok KumarAugust 8, 2017 at 9:19 PM

      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.

      Delete
  4. UnknownAugust 9, 2017 at 12:10 AM

    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. Prof. Dr. T. Ashok KumarAugust 9, 2017 at 7:12 PM

      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.

      Delete
  5. UnknownAugust 9, 2017 at 7:19 PM

    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
  6. UnknownDecember 7, 2017 at 4:32 PM

    This comment has been removed by the author.

    ReplyDelete
  7. UnknownDecember 7, 2017 at 4:38 PM

    Dear Dr. Ashok Kumar,
    Thank you very much for your kind information. I have followed your steps and its working greatly on my Windows 10 OS. Some software's has been updated and its working perfectly.

    ReplyDelete
  8. UnknownDecember 7, 2017 at 7:46 PM

    The only thing is I could not save the image in current working directory. I can save the images only in C:\Python35. Please help me in this regards

    ReplyDelete
    Replies
    1. Prof. Dr. T. Ashok KumarDecember 7, 2017 at 7:56 PM

      It is very simple. Right-click PyMOL icon and click the list 'Run as administrator', to get administrator rights to PyMOL. Now you can be able to save image to the desired location.

      Delete
    2. UnknownDecember 8, 2017 at 11:46 AM

      Thank you very much for your reply. I have already set the Admin rights and tried. But it was not working. It shows error like this: "ScenePNG-Error: error writing "F:/Local Disk E/Stalin/123.png"! Please check directory...

      Delete
    3. Prof. Dr. T. Ashok KumarDecember 8, 2017 at 1:59 PM

      Please check permission in the directory which you are trying to save. For example, read only...

      Delete
  9. UnknownDecember 12, 2017 at 10:49 AM

    Now its working properly. Thank you very much.

    ReplyDelete
  10. Cik ChemistOctober 21, 2020 at 3:36 PM

    why I cannot open the link to download the package?

    ReplyDelete
    Replies
    1. Prof. Dr. T. Ashok KumarOctober 21, 2020 at 9:17 PM

      The author of unofficial windows binaries for Python extension packages repository, Christoph Gohlke have removed the old packages. So, you download latest packages. Watch my video tutorial at https://www.youtube.com/watch?v=m_J-kaImYeM

      I will update the article, according to the new binary package updates.

      Delete
  11. CyanoBacterDecember 4, 2020 at 8:59 PM

    Thanks for this, worked like a charm with a bit of updating of filenames for python 390.

    ReplyDelete

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