How to compile and install Pymol (windows & linux & MAC!) Updated to 1.8.2.0

This tuto explains how to install and compile the last version of Pymol on Windows and Linux.
News : updated to 1.8.2.0 for 64bit systems on 25/04/16

 


 

Windows (1.8.2.0):

Thanks to Christoph Gohlke from the Laboratory for Fluorescence Dynamics, University of California for the precompiled version of pymol available on his website (http://www.lfd.uci.edu/~gohlke/pythonlibs/)

For 64 bits (1.8.2.0):

  • Download and install Python 2.7.9 (and only python 2.7.9)
  • The compilation may fail if you don’t have Virtual C++ compilator for Python : http://www.microsoft.com/en-us/download/details.aspx?id=44266
  • You will need the precompiled version of pymol made by Christoph Gohlke. It’s not user friendly, so I made an archive with all the files and a batch script to install it automatically.
    • 64 bits computers:
    • Once you have installed Python, extract all the files from the archive. All the files needs to be on the same folder.
    • Run install_pymol.bat and voilà! Press a touch to close the windows
    • Now you can launch Pymol from C:/Python27/pymol.exe (default path).If Python is installed on another folder, go to [PYTHONFOLDER]/pymol.exe

For 32 Bits (1.7.5.0):

Since Pymol 1.8.0.0 is not available for 32 bits version, I will keep the 1.7.5.0 for 32bits.
NOTE  : On this version volume renderer (such as .dx maps) is not working with this version on windows. If you want this version you have to downgrade to the 1.7.0.0 or use the linux version, through virtual PC for exemple, or use the 64bit version if your system support it.
Almost the same as 64 bits :

  • Download and install Python 2.7.9 (and only python 2.7.9)
  • Virtual C++ compilator for Python : http://www.microsoft.com/en-us/download/details.aspx?id=44266
  • You will need the precompiled version of pymol made by Christoph Gohlke from the Laboratory for Fluorescence Dynamics, University of California. It’s not user friendly, so I made an archive with all the files and a batch script to install it automatically.
    • 32 bits Computers:
    • Once you have installed Python, extract all the files from the archive. All the files needs to be on the same folder.
    • Run install_pymol.bat and voilà! Press a touch to close the windows
    • Now you can launch Pymol from C:/Python27/pymol.exe (default path).If Python is installed on another folder, go to [PYTHONFOLDER]/pymol.exe

NOTE : the last step of the pymol lib compilation may be long but it’s normal!

NOTE 2 : If you have the error « Python not found »

Some of you have a issue with Python (« Python not found »). My script search the Python Path in the Windows Registry. If Python was not installed correctly maybe the location in the registry will not be the same. In this case, I create 2 other archives with the default python path ( » C:/Python27 « ).

  • If you have this error and python is installed in this directory, you can use this new script and it will work!
  • If you have not installed python in this directory (the default one), you have to modify the script « install_pymol.bat ». To do : just remplace  » C:/Python27  » (without quote) by your current python directory (like  » D:/softwares/python27 « ).

 


Linux (1.8.2.0):

On linux, the installation is a little harder…. But I hope try to simplify it for you :). Good news for non root user! Most of packages needed for PyMOL compilation are usually already installed on Linux session. If not, you still can ask you admin to install it.

1 – Firstable: you need python, python-dev, python-pmw, numpy, freeglut3-dev, libglew-dev, libpng, libfreetype and to avoid to have issues during the compilation, install the build-essential package:

sudo apt-get install python python-dev python-pmw python-numpy freeglut3-dev libglew-dev libpng12-dev libfreetype6-dev build-essential libxml++2.6-dev

2 – Download Pymol source and extract it:

wget http://sourceforge.net/projects/pymol/files/latest/download -O pymol_source.tar.bz2
tar -xvf pymol_source.tar.bz2
cd pymol 

3 – Prepare your installation folder (for me : ~/Softwares/Pymol/) but you can change it.

mkdir -p ~/Softwares/Pymol/
prefix=~/Softwares/Pymol
modules=$prefix/modules

4 – build  and install PyMOL:

 python setup.py build install --home=$prefix --install-lib=$modules --install-scripts=$prefix

5 – Grab a coffee, it can take a while…

6 – Normally, you will have a pymol executable into ~/Software/Pymol. If not check section Issues (bottom of the page).

7 – If you want to run pymol simply by using the « pymol » command you can:

  • If you are root : put the pymol executable in your /usr/bin folder
     sudo cp ~/Softwares/Pymol/pymol /usr/bin/pymol 
  • If you are not root: create a alias :
    echo 'alias pymol="~/Softwares/Pymol/pymol"'  > ~/.bashrc

    Then close and re-open a terminal or:

     source ~/.bashrc 

 

Issues on LINUX

If you don't have a "pymol" executable in your $prefix folder (or pymol folder if you just run python setup.py build install), try these:
  • If it’s not working : check if you have really installed the build-essential package:
     sudo apt-get install build-essential 
  • If you have an error with this line : « error: command ‘x86_64-linux-gnu-gcc’ failed with exit status 1 » (you may have a lot of texte during the compilation, so you have to look weel). It’s because you gcc compilator is set to consider warning like errors. Try :
     export CFLAGS="-Wno-error" 
  • If you have another error like :
     export CFLAGS="-std=gnu++0x" 

    or :

     export CFLAGS="-Wno-error -std=gnu++0x" 
  • If you have other issues (error like « pymol is a directories », cc1 errors etc…) : try to delete Pymol folder, and extract again the pymol archive (try again from step 2).
  • If it’s not working too… I don’t know.. You can send me an email through the Contact page with your error message. I can’t assure that I will fix it, but I will try and if I manage to do it, I will put the solution here.
  • If you see an error during the compilation (with the message « compilation terminated » or something like (« something.h not found« ), it’s maybe because one of the package needed is not installed. Try to run again the command on step 1.

 


MAC OSX (1.8.2.0):

Notes:

  • I don’t own a mac and i’m not a MAC specialist…Theses commands was tested on a OSX 10.11 & 10.9  and you NEED fink installed.
    If some packages aren’t available for you OSX version, I suggest you to use
 fink list | grep {PACKAGE_NAME} 

to replace glew1.3 if it’s not available.
ex :

 fink list | grep glew 
  • Feel free to change installation directory and the pymol alias. It’s only example commands.
  • You must be SUDO with theses commands (or install pymol on another directory than /Programs)!
  • You must have an Xquartz installed (or X11 depending your OS X version)

 


sudo fink install python27 numpy-py27 pmw-py27 mesa mesa-shlibs system-pkgconfig-libpng15 freetype219 freetype219-shlibs freeglut2 freeglut2-shlibs glew1.13 glew1.13-shlibs wget tcltk-dev tcltk-shlibs
cd ~/Downloads/
wget http://sourceforge.net/projects/pymol/files/latest/download -O pymol_source.tar.bz2
tar xvf pymol_source.tar.bz2
cd pymol
sudo mkdir -p /Programs/Pymol.app
prefix=/Programs/Pymol.app
modules=$prefix/modules
sudo /sw/bin/python2.7 setup.py build install --home=$prefix --install-lib=$modules --install-scripts=$prefix
echo "alias pymol='/Programs/Pymol.app/pymol'" > ~/.bash_profile
source ~/.bash_profile

Issues :

  • If you have an error like « libpng warning: Application built with libpng-1.5.23 but running with 1.6.19 » : it’s because a more recent library of libpng (or other) was already installed.
    You can remove the one you want with « fink remove [package_name] ».

Have fun on Pymol 🙂
Thibault.

Avec mots-clefs , , , , .Lien pour marque-pages : permalien.

88 réactions à How to compile and install Pymol (windows & linux & MAC!) Updated to 1.8.2.0

  1. blake a écrit:

    Great post on compiling pymol from Golke’s .whl. I followed all the steps in your .bat file (without your files — I was using the updated v1.7.5 pymol files from Golke’s website) and was able to generate the PyMOL.exe executable in my PYTHONPATH folder.

    However, when double-clicking on it, PyMOL does not load. It also will not load when I type ‘PyMOL.exe’ from the PYTHONPATH folder in the MS-DOS shell. Do you have an idea why this is happening? Thanks!

    • Thibault Tubiana a écrit:

      Hi!
      Thank you for this information! I didn’t notice that there was a new version of Pymol, and that’s right, it (was :p) not working!

      After few tries, I managed to find that this new version need Numpy 1.9.2+mkl to be executed.

      I upgraded my archive with this package (for 32 and 64 bits) so now all that you have to do is to download again the archive and run (double click) on install_pymol.bat =D I tried on a clean install and it (should) works!

      Let me know it works or not 🙂

      • blake a écrit:

        Thanks so much for the quick reply! That was what was missing for me — I didn’t even think to check against the version of numpy that was installed. I had simply let pip install numpy automatically for me, not the .whl that was listed on Golke’s website. I’ve got pymol working now.

        Hopefully other people can find your website — I was absolutely clueless about how to solve this problem (Golke’s website had precompiled installation packages until very recently) and I’m not a python expert, so I really appreciate your help.

  2. Thibault Tubiana a écrit:

    You are welcome 🙂 I’m happy to see that people use my scripts to have Pymol!!

  3. Rute Félix a écrit:

    Hello, I am trying to install pymol following your instructions that I find that are very easy to understand, but I am a first user and when I click on install_pymol.bat i get a message saying that it can´t find Phyton 2.7 and that a should chek my installation, and I think that i put the pymol package inside the Phyton folder. Do you have any ideia what i could be doing wrong.
    Thank you

    • Thibault Tubiana a écrit:

      If you have this message, it means that you the script can’t find Python 2.7. Did you install it with the link that I gave ?
      Maybe try to re-install python :

      1 – first check if you have this folder : « C:/Python27 »)
      2 – if you have it, uninstall python, then install it again with this link (https://www.python.org/ftp/python/2.7.9/python-2.7.9.amd64.msi) or (https://www.python.org/ftp/python/2.7.9/python-2.7.9.msi) and install it again. During the installation, they will ask you if you want to install it for all users, say yes!
      3 – try to run again the script « install_pymol.bat »

      I check on several configuration and each time it worked. So normally it should be ok.

      • Rute Félix a écrit:

        thank you for your quick response. I did everything that you suggested but i had the same result. I am still unable to install the pymol. I don’t know what i am doing wrong. do i need to install pymol first somewhere? thank you

        • Thibault Tubiana a écrit:

          Did you check that you have downloaded the good version for your computer (32 or 64bit?) To check : click on Start, then right click on Computer and then Properties. Check the line « System type ».

          If you have 32 bit : download Python 2.7.9 for 32 bit (check my link) AND the 32 bit archive.

          If you have 64 bit : download Python 2.7.9 for 64 bit (check my link) AND the 64 bit archive.
          _________
          If it’s not that, did you extract all the files from the archive in the same folder ?

          Can you paste me the error message ?

  4. Rute Félix a écrit:

    hello, I did all that you said. My computer is 32 bits and i downloaded the 32 bit python and the respective pymol archive. I put the pymol folder inside the Python folder, and if i open a cmd window I can see the pymol file inside the Python (C:\Python27\Pymol_win_32>).

    if i click directly on the install_pymol.bat the message error is : Can’t find Python 2.7. Please check your installation : install Python 2.7

    Is it possible that i am not using a pymol executable file, or whl is the same, do i need some sort of program to open this files…

    I think Python is ok, but i don’t know this program… I think that i need an executable file from pymol nut all i can find is whl files and when a click on them a cmd windom opens and closes imediatly and nothing happens…

    • Thibault Tubiana a écrit:

      My script will use python to compile the .whl file and then create the pymol executable. So if the scrypt can’t find python, it can’t generate pymol executable.

      The script will try to find the python path on this registry key : HKEY_LOCAL_MACHINE\SOFTWARE\Python\PythonCore\2.7\InstallPath

      Which distribution do you have? XP/VISTA/SEVEN ? I use Seven so maybe the python registry key is not the same….

  5. Rute Félix a écrit:

    Hello again,

    my computer is windows 7, so i really do not understand what I am doing wrong.

    How can i find out if that registry key exist in my computer?

    I was able to find a pymol executable file (an old one pymol-1.5.0.3.win32-py2.7.exe ) but it worked and pymol program is working now (the old version), so i really don’t understand.

    Should I try your script now that i know python is working?

    Thank you for all your help 🙂

  6. Thibault Tubiana a écrit:

    Yes Pymol 1.5.0.3 is an old version and you can easyly find an executable.

    This is very weird what’s happenig.

    Can you make a last try with this archive => http://tubiana.me/files/Pymol_win_32-rute.rar ?
    I wrote the python path in the script instead of searching it (« C:/Python27/ ») If it’s work, you should see « pymol.exe » in C:/Python27/…. (finger crossed…)

  7. Rute Félix a écrit:

    Hello again,

    it worked ;)))) I have now the PyMOL 1.7 working in my computer.

    Thank you very much 😉 you were great 😉

    Now I only need to start working with my proteins and try to understand it 😉

    I really really appreciate your help

    Best
    Rute

  8. Patty a écrit:

    Hi,

    I tried to install Pymol with your files on my Win7 64.
    Doing everything as you said, I get the error message that Python2.7 cannot be found.

    Can you tell me what I should do now?
    Thanks in advance 🙂

    • Thibault Tubiana a écrit:

      Hi!

      It’s the second time that someone report me this issue.. I don’t know why this happen, but chech again my tutorial, I wrote a little word why you can have this issue and I add 2 new archives with a fixed script. The difference between the « PythonFixed » archives and the sandard ones is that I wrote the default python (C:/Python27) instead of searching it and put it in a variable. If your python installation is not this one (« C:/Python27) replace it by your Python Path.

      Hope that it works now 🙂

      • Alexander Thrun a écrit:

        I don’t know if it’s still a problem, but better safe than sorry 😉 I had to fix the

        for /f « tokens=4 »

        part to

        for /f « tokens=3 »

        because the reg query only gives me three tokens, with the third one being the path to the python directory. With that everything works fine. Oh, and btw I’m using Windows 7 Enterprise 64 bit. Don’t know if Enterprise gives different tokens in the cmd? Nevertheless, thank you for the scripts!

  9. Patty a écrit:

    Thanks a lot for your very quick response 🙂

    this one worked out for me! 🙂

  10. eMKi a écrit:

    Dear Thibault,

    thank you for this nice tutorial.
    In case you also figured out how to install Freemol add-ons on linux I would be very gracefull if you could post short instructions.
    I would like use esspecially MPEG encode option.

    Thanks!

    • Thibault Tubiana a écrit:

      Thank you 🙂

      I didn’t try to install Freemol add-on on Linux.. I will take a look if I have time.
      To make video I use the PNG option (File > Save movie as > PNG images or « mpng [name] » command) and then I use FFMPEG to convert png to video. With this method I can control the resolution, quality, framerate and the size of my video.

      If you want to install FFMPEG :

      sudo add-apt-repository ppa:kirillshkrogalev/ffmpeg-next && sudo apt-get update
      sudo apt-get install ffmpeg

      And to convert pictures to mpg video :
      ffmpeg -r 25 -f image2 -i protein_%03d.png -qscale:v 1 video.mpg
      (assuming the name is like »protein_000.png », %03d is the number of numbers in your file name)
      You can adjust the quality/size of the video with « -qscale:v 1 » (bigger the number is, smaller the video is). « -r » is the framerate.

      If you have time and you want beautiful images, you can activate the ray-tracing for each frame with the command « set ray_trace_frames=1 », That’s what I do.

      I hope it can help you 🙂
      Thibault.

  11. eMKi a écrit:

    Hi,

    thank you for this suggestion.
    So far I have been using mencoder for the same purpose.
    I’ll give FFMPEG a spin.

    I find that already the ‘draw’ function enhances the image quality considerably and is less resource hungry than ‘ray’. It is a compromise of course.

    One more thing. How come you prefer FFMPEG from this specific ppa and not the one in the official repositories?

    Thanks.

  12. Ed Hutchinson a écrit:

    This was incredibly helpful – thank you very much!

  13. Markus Heller a écrit:

    Hi Thibault,

    just curious, do you have pymol 1.7.6 under Windoze 7 in the works?

    Thanks and Cheers
    Markus

  14. Catie a écrit:

    Hi Thibault,

    Your instructions are very clear and helpful. Is there any reason why this approach would not work on Windows 10?

  15. Thorsten a écrit:

    Doesn’t work at all:

    C:\Python27\pymol\Pymol_win_64>install_pymol.bat
    ERROR: The system was unable to find the specified registry key or value.
    Can’t find Python 2.7. Please check your installation : install PYTHON 2.7
    Press any key to continue . . .

    C:\Python27\pymol\Pymol_win_64>python –version
    Python 2.7.10 :: Anaconda 2.3.0 (64-bit)

  16. Wei Wang a écrit:

    Hi Thibault,

    Have you tried to build pymol in a virtualbox linux guest? I’m using scientific linux 7 on a win 7 host. I tried several times but experienced some problem. The GUI part does not show up. And reinitialization will set pymol to not responding for further fetching another pdb file.

    • Thibault Tubiana a écrit:

      Hi Wei,

      I never tried this.. but Scientific Linux 7 is based on a RedHat system, maybe the packages that you have to installed are different… When the GUI part does not show up it’s usually because python-tk is not installed or not correctly linked (I’ve also this issues on the python3 version of Pymol 1.8 and I didn’t fix it yet…)

  17. Mark a écrit:

    Hello Thibault,

    Thank you for the wonderful tutorial. Very helpful. I attempted to install PyMOL 1.8 on 64 bit Win 10 machine but it doesn’t recognize the platform. I was able to install the 32 bit version of PyMol successfully using your tutorial.

    Below are the errors that I received for the amd64.whl files.

    I have at least two difference in my protocol compared to yours that I would like to rule out as the source of error if possible.

    1. I installed Python 2.7.11 instead of 2.7.9. I assumed the necessity of Python 2.7 is in comparison to Python3, but maybe the .whl files need Python 2 .7.9 specifically?

    2. I’m running Windows 10, and it appears from reading most of the forum sites, etc that these .whl files were precompiled on Windows 7? I’m not especially proficient in Windows so I’m not aware of the difference between the two OSs with regards to .whl files.

    Thanks again for your tutorial. Regardless of the issue with PyMOL 1.8.0, the 1.7.6 32 bit version works nicely with my 3D Vision setup which is my main need right now.

    Sincerely,

    Mark

    C:\PyMOL_installation>C:\Python27\Scripts\pip.exe install numpy-1.9.3+mkl-cp27-none-win_amd64.whl
    numpy-1.9.3+mkl-cp27-none-win_amd64.whl is not a supported wheel on this platform.

    C:\PyMOL_installation>echo Pymol lib installation
    Pymol lib installation

    C:\PyMOL_installation>C:\Python27\Scripts\pip.exe install pymol-1.8.0.0-cp27-none-win_amd64.whl
    pymol-1.8.0.0-cp27-none-win_amd64.whl is not a supported wheel on this platform.

    C:\PyMOL_installation>echo PWN Graphic interface installation
    PWN Graphic interface installation

    C:\PyMOL_installation>C:\Python27\Scripts\pip.exe install pymol_launcher-1.0-cp27-none-win_amd64.whl
    pymol_launcher-1.0-cp27-none-win_amd64.whl is not a supported wheel on this platform.

    • Thibault Tubiana a écrit:

      Hi mark! Thank you for your comment 🙂

      I think your problem maybe come from python 2.7.11 because I’m running on Windows 10 64bits, and it works for me (with python 2.7.9).
      I assume the wheel package was compiled on a 2.7.9 and so it works only on this version..

      Hope it will work better with that!

      Sincerely,
      Thibault.

    • eMKi a écrit:

      Dear Mark,

      in my experience with the files provided on this site you need specifically Python 2.7.9.

      I am glad you got 3D vision working on Win. It was extremely time consuming in my case.

      Kind regards!

  18. Fatima a écrit:

    Dear Thibault,

    Thank you for this tutorial. I’m trying since two days and can’t install pymol. My windows is 8.1 and system type is 64x. I installed python successfully with the path you described and extracted all pymol files in the same folder with python, I get the error msg; Can’t fine python 2.7 please check your installation.
    Im really devastated and my work is pending a week ago trying to get pymol on my device 🙁

  19. Fatima a écrit:

    OMG the fixed one worked!
    Thank uuuu soooo much : » »)
    You’re a goddess!

  20. gianluca a écrit:

    Hi,

    it works but I have only the graphical windows. Do you know how I can get the menu window ? is there sommething that i should modify in the installation ?
    best regards

  21. Lea a écrit:

    Hello! I installed 1.8 in Mac and the program opens however the toolbar window or menu window where I can open the file appears to non-functional as it is purely displayed in white. It was initially missing but I installed pmw and somehow it opens but not really functioning. Do you know what might’ve happened wrong in the script?

  22. Quartz a écrit:

    Can someone help me with the MAC? I’ve installed fink, xquartz, and am running 10.11.

    I copy paste the code

    sudo fink install python27 numpy-py27 pmw-py27 mesa mesa-shlibs system-pkgconfig-libpng15 freetype219 freetype219-shlibs freeglut2 freeglut2-shlibs glew1.13 glew1.13-shlibs wget tcltk-dev tcltk-shlibs
    cd ~/Downloads/
    wget http://sourceforge.net/projects/pymol/files/latest/download -O pymol_source.tar.bz2
    tar xvf pymol_source.tar.bz2
    cd pymol
    sudo mkdir -p /Programs/Pymol.app
    prefix=/Programs/Pymol.app
    modules=$prefix/modules
    sudo /sw/bin/python2.7 setup.py build install –home=$prefix –install-lib=$modules –install-scripts=$prefix
    echo « alias pymol=’/Programs/Pymol.app/pymol' » >> ~/.bash_profile
    source ~/.bash_profile

    and this is the error i get

    09-020-7974:pymol NAME$ source ~/.bash_profile
    -bash: /Users/NAME/.bash_profile: line 21: unexpected EOF while looking for matching ` »
    -bash: /Users/NAME/.bash_profile: line 22: syntax error: unexpected end of file

    • Thibault Tubiana a écrit:

      It looks like the line
      alias pymol=’/Programs/Pymol.app/pymol’
      is not weel formated in your file ~/.bash_profile
      Open it and check yout last line. Apparently there is an « ` » somewhere and your shell is waiting for another one (that what « unexpected EOF while looking for matching ` » means)

      Sometimes when you copy past commands the ‘ is changed in `.

  23. Quartz a écrit:

    Appreciate your reply, but I can not figure it out. I don’t think there is a hidden ` in the code I pasted. Is this bash file somewhere separate that I can open?

    This is another error I get, maybe related. It happens after running python:

    09-020-7974:Downloads NAME$ cd pymol
    09-020-7974:pymol NAME$ sudo mkdir -p /Programs/Pymol.app
    09-020-7974:pymol NAME$ prefix=/Programs/Pymol.app
    09-020-7974:pymol NAME$ modules=$prefix/modules
    09-020-7974:pymol NAME$ sudo /sw/bin/python2.7 setup.py build install –home=$prefix –install-lib=$modules –install-scripts=$prefix
    fatal: Not a git repository (or any of the parent directories): .git
    svn: E155007: ‘/Users/NAME/Downloads/pymol’ is not a working copy

    Many thanks:)

    • Thibault Tubiana a écrit:

      If you open a new terminal you have the same error message concerning the bash_profile file, there is definitely a syntax issue in it. Maybe not in the code that you paste but inside the file .bash_profile in your home directory

      And for the second error I don’t know; You have a git & svn issue… But in my knowledge the building and install don’t use git or svn…

      I don’t own a mac so I can’t help you on that :/

  24. arien a écrit:

    Hi,
    I have problem on Ubuntu 14.04:

    ~/Softwares/Pymol$ ./pymol
    Traceback (most recent call last):
    File « /home/arien/Softwares/Pymol/modules/pymol/__init__.py », line 71, in
    import pymol
    File « /home/arien/Softwares/Pymol/modules/pymol/__init__.py », line 521, in
    import pymol._cmd
    ImportError: /home/arien/Softwares/Pymol/modules/pymol/_cmd.so: undefined symbol: png_check_sig

    Any ideas? 🙁
    Thank you for this nice tutorial anyway.

  25. André a écrit:

    Thxs a lot for your help!!!

    Can you also tell us how to install the precompiled whl file (which you provided as a batch file) so we can install the updated version?

    thx

    best regards

  26. André a écrit:

    I’ve tried to to adjust your batch file for the new update 1.8.1.2, but it says:

    UnsupportedWheel: pymol-1.8.1.2-cp27-cp27m-win_amd64.whl is not a supported wheel on this platform.

    also tried it with python 3.5 without success.

    did the whl change somehow?

  27. André a écrit:

    ok, got it, for windows:
    there is a new
    numpy-1.10.4+mkl-cp27-cp27m-win_amd64.whl
    that has to be used,
    as well upadate:
    python 2.7.11
    and update pip via cmd

  28. Alexander a écrit:

    Thank you, Merci.
    Works like a charme – but: I had to set « PYTHONPATH » manually in the environment variables (Control Panel System, Advanced System Settings, Advanced. (Though it is correctly set in the registry).
    Anyway, thanks again.

    • André a écrit:

      That is actually quiet important! Thank you!!!

      Does anyone know why stereoscopic 3d (quadbuffered) is not working in this compiled versions? It is detected and also enabled by Pymol.

      When using the educational version (compiled by schroedinger) on the same PC, stereoscopic 3D is working, although their version is older 1.7.4.5

      thanks

  29. Annie a écrit:

    Hello,

    I am working to install the open-source Py_MOL for a project, and after extracting the files using WinZip to a folder on the C:\ drive, I get the following error: « Numpy MKL Installtion
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    Wheel installation
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    Pip Upgrade
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    PWN Installation (for tkinter windows)
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    Pymol lib installation
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    PWN Graphic interface installation
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    DONE — To run Pymol Launch :
    C:\Program Files (x86)\CambridgeSoft\ChemOffice2015\ChemScript\Libpymol.exe
    Press any key to continue . . . » Any thoughts as to the error would be greatly appreciated.

    Many thanks!

    • Thibault Tubiana a écrit:

      Hi!

      Did you isntall python 2.7?
      If yes try to reinstall in a folder with no space for example C:\Python27.
      It sounds like it is install in « C:\Program Files » and Windows batch command don’t like space.

  30. Joao a écrit:

    Hi Thibault,
    Just a quick message to thank you for this! It helped a lot!
    Best Wishes,
    joao

  31. RayCharlZ a écrit:

    It didn’t work for me. It only prompts « Wheel installation » and does not seem to do anything else. I have Python27 and Virtual C++ on my machine and I am trying to install the Windows 64 bits version, running on Windows 10. I tried to google this problem but I didn’t find anything.

  32. Fabian a écrit:

    Wow really nice i will try this ASAP
    Is there any way to get this done with python 2.7.10?
    This is what i currently use and i do not feel to reinstall it at the moment!

    All the best

  33. milo a écrit:

    Hi, I did everything as you said, but there was a message it can´t find Phyton 2.7 and that a should chek my installation. I saw there were also someone else had this problem, but my system is win 10, so I don’t know how to do next step. Thank you very much.

  34. milo a écrit:

    I did everything as you said, but I still get the message it can´t find Phyton 2.7 and that a should chek my installation. I saw someone else
    who also had this problem, but my computer system is win10, 64bit, so what should I do next step? Thank you very much.

  35. milo a écrit:

    Thanks for your note, I made it work. Thanks a lot for your share

  36. Marion a écrit:

    Using Windows 10 64 bits, it worked when I changed the tokens=4 to tokens=3 in install_pymol (with tokens=4 I was getting the error message that Python2.7 cannot be found).
    Thank you so much!!

  37. Heberth a écrit:

    I installed PyMOL and I’m able to run it. But it runs poorly and with too much lag to be usable. Do you know something I can do to fix this?

  38. André a écrit:

    Does anyone know why stereoscopic 3d (quadbuffered) is not working in this compiled versions? It is detected and also enabled by Pymol.

    When using the educational version (compiled by schroedinger) on the same PC, stereoscopic 3D is working, although their version is older 1.7.4.5

    thanks

  39. Pingback:Installing latest version of Pymol from source? - ubuntutextbook

  40. Dimitris a écrit:

    Hi,

    I am trying to install pymol but I am getting the message below. I have installed python in a folder without space (I saw a reply of yours to someone with similar error) and then extracted the pymol files in a separate (from python) folder on C:\ drive.

    BTW, great job!

    Thanks!

    ERROR: The system was unable to find the specified registry key or value.
    Wheel installation
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    Pip Upgrade
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    PWN Installation (for tkinter windows)
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    Numpy MKL Installtion
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    Pymol lib installation
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    PWN Graphic interface installation
    ‘C:\Program’ is not recognized as an internal or external command,
    operable program or batch file.
    DONE — To run Pymol Launch :
    C:\Program Files (x86)\CambridgeSoft\ChemOffice2012\ChemScript\Libpymol.exe
    Press any key to continue . . .

  41. urgent a écrit:

    hi my pc is windows 8 and 64 bit and i tried everything but i couldnt install please help me urgent

  42. Thibault Tubiana a écrit:

    Did you install python 2.7.9 ?
    I can’t help you if you don’t give me any information on what happened

  43. python a écrit:

    hi
    my computer is 32 bit windows 10 and i ty to install but it gives the eror as cant find the pyton what should i do
    and i try the pymol_win_32-rote rar file it work but i still couldt find the pymol fle when i searched as C:/Python27/pymol.exe

  44. anon a écrit:

    Hi.

    In case it is helpful to anyone.

    After downloading the « fixed » zip file, I found that « pymol_launcher-1.0-cp27-none-win_amd64.whl » and « pymol-1.8.2.0-cp27-cp27m-win_amd64.whl » were corrupted, which prevented the installation of pymol. I substituted those files for the ones found in the « unfixed » zip file and it worked all right.

  45. Petra a écrit:

    Hi,
    I would like to express endless gratitude, because without this i would never be able to install pymol. So thanks very much.

  46. Rob a écrit:

    Hi Thibault,

    Thank you so much for this, it works beautifully.

    I just had a quick question on where the files for PyMol are actually saved. I am trying to install ProMol as a plugin in PyMol, but I am unable to find the directory of PyMol’s files.

    I am using windows 7 on a 64 bit computer.

  47. Thibault Tubiana a écrit:

    Hi! You’re welcome 🙂
    It is in your python27 repertory and then in Lib\site-packages\pymol.
    For example :
    C:\Python27\Lib\site-packages\pymol

  48. Rob a écrit:

    I actually have one more question, if you could help me out again. I installed ProMOL-5.4-r419.exe from sourceforge and was able to get all the plugins except ProMol itself. It is listed as a possible plugin, but every time I click load I get the error « Unable to initialize plugin ‘ProMol’ (pmg_tk.startup.ProMol) ».

    Any idea why this is?

  49. Vlad a écrit:

    Hi Thibault,

    First of, thank you so much for this tutorial, but I’m still having problems installing pymol. I used the pythonfix Pymol 64-bit. I attempted to install it but all I got was this message:

    Wheel installation
    Requirement already satisfied (use –upgrade to upgrade): wheel in c:\python27\lib\site-packages
    You are using pip version 8.1.1, however version 9.0.1 is available.
    You should consider upgrading via the ‘python -m pip install –upgrade pip’ command.
    PWN Installation (for tkinter windows)
    Requirement already satisfied (use –upgrade to upgrade): Pmw==2.0.0 from file:///C:/Python27/Pymol_win_32-rute/Pymol_win_32/Pmw-2.0.0-py2-none-any.whl in c:\python27\lib\site-packages
    You are using pip version 8.1.1, however version 9.0.1 is available.
    You should consider upgrading via the ‘python -m pip install –upgrade pip’ command.
    Numpy MKL Installtion
    numpy-1.9.2+mkl-cp27-none-win32.whl is not a supported wheel on this platform.
    You are using pip version 8.1.1, however version 9.0.1 is available.
    You should consider upgrading via the ‘python -m pip install –upgrade pip’ command.
    Pymol lib installation
    pymol-1.7.5.0-cp27-none-win32.whl is not a supported wheel on this platform.
    You are using pip version 8.1.1, however version 9.0.1 is available.
    You should consider upgrading via the ‘python -m pip install –upgrade pip’ command.
    PWN Graphic interface installation
    pymol_launcher-1.0-cp27-none-win32.whl is not a supported wheel on this platform.
    You are using pip version 8.1.1, however version 9.0.1 is available.
    You should consider upgrading via the ‘python -m pip install –upgrade pip’ command.
    DONE — To run Pymol Launch :
    C:\Python27\pymol.exe
    Press any key to continue . . .

    I would very much appreciate your reply. Thanks again

  50. Thibault Tubiana a écrit:

    If you are on a 64bits computer, use the 64bits archive. I can see through theses error that you have the 32bits archives (« numpy-1.9.2+mkl-cp27-none-win32.whl » ==> win32).

  51. Antonis a écrit:

    Dear Thibault,

    Thank you for this nice tutorial. I successfully installed the PyMOL following your instructions. However when i run a PyMOL script or when i load a PDB file and tell the program to show me spheres, the program doesn’t respond and it leaves the place empty. Also the program says: cannot find shader ‘cylinder’

    Can you help me please?

  52. Zolo a écrit:

    Hello,

    Could you help me please. I am trying to install it. After installing phyton and extacting pymol file (32bit) then clicking on install_pymol.bat file i see a window saying it is not recognised internal or external command, operable program batch file and at the end it says to run pymol launch: chambridgesoft\chemoffice2015\chemscript\libpymol.exe and i could not find it when i go there. So i am stuck.

    Thanks

  53. Sahj a écrit:

    Hi!
    First off, thank you for this tutorial, but I have a problem.
    I have downloaded and installed Python and i have also downloaded the Pymol 64 bits fixed compiled archive. I have windows 8.1 by the way.
    anyways, after that i double click on install_pymol.bat and I think that it’s working because i don’t get any message about that some file can’t be found.

    it ays: To run pymol Launch :
    DONE — To run Pymol Launch :

    C:\Python27\Pymol>echo C:\Python27\pymol.exe
    C:\Python27\pymol.exe

    C:\Python27\Pymol>pause
    Press any key to continue…

    so what do i do now exactly?

    Thank you in advance! 🙂

  54. Javier a écrit:

    Hello, trying to install PyMOL on Windows10 here…
    – I downloaded and installed python-2.7.9.amd64.msi
    – I checked the registry on HKEY_LOCAL_MACHINE\SOFTWARE\Python\PythonCore\2.7\InstallPath and C:\Python27\ is there.

    However, when trying to run the .bat script, I get the message:
    « The system cannot find the path specified ». Here’s the full output:
    —————
    Wheel installation
    The system cannot find the path specified.
    Pip Upgrade
    The system cannot find the path specified.
    PWN Installation (for tkinter windows)
    The system cannot find the path specified.
    Numpy MKL Installtion
    The system cannot find the path specified.
    Pymol lib installation
    The system cannot find the path specified.
    PWN Graphic interface installation
    The system cannot find the path specified.
    DONE — To run Pymol Launch :
    C:\Python27\Libpymol.exe
    Press any key to continue . . .
    —————

    … and I cant find Libpymol.exe anywhere in my computer

    By the way, do you think we should try to run the newer version of numpy, numpy-1.11.3+mkl-cp27-cp27m-win_amd64.whl ?

    What could be wrong? Thank you so much…
    Javier

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