This tuto explains how to install and compile pymol 2.5.0 on Windows, Mac and Linux.
UPDATE: 02/02/2023 : After thousands of visits in the past years, a windows archive was downloaded more than 70K times, everything was wiped and updated for a new installation with CONDA =D
Windows (2.5.0):
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/)
The easiest way to install pymol on windows now, is to install it through python 3.7+
- STEP 1 (optional if you already have a python 3.7 installed)
Download Anaconda (or Miniconda if you prefer a small and more basic python installation) in version 64bits and version 3.7 to 3.11 maximum - STEP 2 : open « anaconda/miniconda prompt » from the windows start button
- STEP 3 Write this code :
import sys
import os
import subprocess
sysverlist=sys.version.split(".")
ver=sysverlist[0]+sysverlist[1]
#Installpymol
pymolLink=f"https://download.lfd.uci.edu/pythonlibs/archived/pymol-2.5.0-cp {ver}-cp{ver}-win_amd64.whl"
subprocess.check_call([sys.executable,"-m","pip","install",pymolLink])
launcherLink=f"https://download.lfd.uci.edu/pythonlibs/archived/pymol_launcher-2.5-cp {ver}-cp{ver}-win_amd64.whl"
subprocess.check_call([sys.executable,"-m","pip","install",launcherLink])
- STEP 4 : pymol is now installed in your python directory. To know where it is write
os.path.dirname(sys.executable)- You can now create a shortcut of pymol in your desktop or anywhere… You can also write « pymol » directly on the PATH bar in your windows explorer window.
Linux AND MAC!
On linux and mac, the best way is to install pymol-open-source Through Conda.
If you have anaconda/miniconda already installed, go to step 2.
STEP 1: (optional if you already have miniconda/anaconda) Install miniconda.
MAC
#Downloading the latest Miniconda installer for macOS. Your architecture may vary.
curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
Or if you have LINUX
#Downloading the latest Miniconda installer for Linux. Your architecture may vary.
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
say YES when you have the question about the initialization.
STEP 2: install pymol
Now you can install pymol with the command
conda install -c conda-forge pymol-open-source
STEP 3: run pymol
Now you can run pymol from your terminal with the command pymol
BONUS: for mac users if you want to create a shortcut, follow « How to save a macos terminal command as a shortcut using automator » tutorial on https://siytek.com/macos-terminal-command-as-a-shortcut/
Have fun on Pymol 🙂
Thibault.
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!
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 🙂
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.
You are welcome 🙂 I’m happy to see that people use my scripts to have Pymol!!
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
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.
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
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 ?
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…
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….
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 🙂
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…)
Hey Thibault Tubiana,
Thank you so much for the personalized script. Nothing worked for me, but this, finally!!
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
Great =D Happy to ear that 🙂
Have fun now with Pymol =D
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 🙂
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 🙂
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!
This edit worked for me as well. Win7/64 Enterprise
Thanks, it also worked for me on Win 8.1/64.
Thanks a lot for your very quick response 🙂
this one worked out for me! 🙂
Great 🙂 Happy to hear that 🙂
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!
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.
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.
This was incredibly helpful – thank you very much!
Hi Thibault,
just curious, do you have pymol 1.7.6 under Windoze 7 in the works?
Thanks and Cheers
Markus
Hi Markus,
just download the 1.7.6 version of PyMOL from http://www.lfd.uci.edu/~gohlke/pythonlibs/ and put it in the extracted folder with the installation files you downloaded from here. Replace the 1.7.5 in the bat file with 1.7.6 (simply open with Notepad). It then works in the same way as described above.
Hi Thibault,
Your instructions are very clear and helpful. Is there any reason why this approach would not work on Windows 10?
Hi!
Thank you 🙂
I have a computer on Windows 10 and it works for me…
Do you get an error ?
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)
Hi,
It didn’t work because you use the Anaconda version of python, which is declared differently on the registry.
I suggest you to install the regular python version that I gave on this tuto (https://www.python.org/ftp/python/2.7.9/python-2.7.9.amd64.msi)
Thibault.
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.
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…)
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.
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.
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!
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 🙁
OMG the fixed one worked!
Thank uuuu soooo much : » »)
You’re a goddess!
You are welcome 🙂
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
Hi!
On wich OS did you install pymol ? (windows/mac/linux?)
Pymol use TCL/TK for the menu windows, so maybe it is not installed on you computer?
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?
Did you install all required packages ?
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
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 `.
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=$prefix
fatal: Not a git repository (or any of the parent directories): .git
svn: E155007: ‘/Users/NAME/Downloads/pymol’ is not a working copy
Many thanks:)
If you open a new terminal you have the same error message concerning the bash_profile file, there is definitely a syntax issue in it. Maybe not in the code that you paste but inside the file .bash_profile in your home directory
And for the second error I don’t know; You have a git & svn issue… But in my knowledge the building and install don’t use git or svn…
I don’t own a mac so I can’t help you on that :/
No problem, thanks for the help. I hate working with these machines but it’s my work computer so..
I’ll post the fix if I find it
Hi,
I have problem on Ubuntu 14.04:
~/Softwares/Pymol$ ./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.
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
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?
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
Thank you for these info (and sorry for the delay) 🙂
I upgraded the package.
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.
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
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!
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.
Hi Thibault,
Just a quick message to thank you for this! It helped a lot!
Best Wishes,
joao
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.
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
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.
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.
Thanks for your note, I made it work. Thanks a lot for your share
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!!
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?
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
Ping :Installing latest version of Pymol from source? - ubuntutextbook
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 . . .
Hi,
I used the pymol fix file and it’s now working so please don’t bother replying.
Thanks again.
hi my pc is windows 8 and 64 bit and i tried everything but i couldnt install please help me urgent
Did you install python 2.7.9 ?
I can’t help you if you don’t give me any information on what happened
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
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.
Hi,
I would like to express endless gratitude, because without this i would never be able to install pymol. So thanks very much.
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.
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
Thank you very much! I also really appreciate your quick response.
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?
I’m sorry I don’t know, I try to install it too and I got the same error. I think it will be nice to contact the developpers to fix it.
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
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).
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?
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
Try to use the « pythonfixed » version. Maybe chemoffice install a python library detected by the installation batch.
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! 🙂
Hi,
If you go to the folder C:\Python27 you will have pymol.exe. Double click on it to launch pymol 🙂
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
The file « Pymol 64bits 1.8 — PythonFixed » worked like a charm.
Thank you!!
Javier
Merci beaucoup!
error
C:\Pymol_win_64\Pymol_win_64>install_pymol.bat
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)\PerkinElmerInformatics\ChemOffice2016\ChemScript\Libpymol
.exe
Press any key to continue . . .
First, thank a lot for your guides on how to install Pymol on Windows. I’ve used them a lot.
Regarding Pymol on OS X:
Fink now has 1.8.7 in its respositories. Therefore the easiest way to install it is:
1) install Fink, Xcode, Xquartz
2) install python27 via Fink
3) install pymol-py27 via Fink (this will also pull all the dependencies)
I just wasted an entire evening trying to compile Pymol under Sierra just because I assumed that Fink would have v. 1.7. Save some time – don’t be me. >.<
Hi!! Thanks for the tutorial! Iḿ using it to install version 1.8.6
BUT iḿ having an issue when the compilation starts a fatal error pops up :
In file included from contrib/mmtf-c/mmtf_parser.cpp:31:0:
contrib/mmtf-c/mmtf_parser_private.h:38:23: fatal error: msgpack.hpp: No such file or directory
compilation terminated.
error: command ‘c++’ failed with exit status 1
Do you know how to fix this?
Hi!! I’ve found the exact same error. Did you found any solution?
Thanks!
I am trying to install pymol on under osX 10.9.5.
I followed your instructions:
1) installed fink
2) used fink to install pymol27, mesa…
Here I couldn’t get system-pkgconfig-libpng15 but replaced it with system-pkgconfig-libpng16.
3) recovered pymol-v1.8.6.0.tar.bz2 from sourceforge
However, when I start the compilation I got the error:
In file included from contrib/mmtf-c/mmtf_parser.cpp:31:
contrib/mmtf-c/mmtf_parser_private.h:38:10: fatal error: ‘msgpack.hpp’ file not found
#include
^
1 error generated.
error: command ‘g++’ failed with exit status 1
Can you help in identifying where I can get the missing file?
I was having SO much trouble until I found out you had a FIX for the install_pymol.bat file. I didn’t think to read to the end AFTER Mac and LINUX since I was using Windows. Thank you! I’m so happy to have it running. You really made the installation easy for a beginner like me!
This was great and straightforward! Thanks for the instructions!
Hi Thibault,
Thank you for this great resource. This is especially useful for mac users as homebrew and macports are currently failing to build pymol.
Just a note I was unable to build pymol on mac using your instructions. I modified slightly and it built ok on OSX sierra :
line 1, as already noted by FXB system-pkgconfig-libpng16 is now provided by fink:
sudo fink install python27 numpy-py27 pmw-py27 mesa mesa-shlibs system-pkgconfig-libpng16 freetype219 freetype219-shlibs freeglut2 freeglut2-shlibs glew1.13 glew1.13-shlibs wget tcltk-dev tcltk-shlibs
system-pkgconfig-libpng16
line 9, fink can’t supply the correct msgpack, but this is optional so can be turned off in the build – I’m not sure how much of an impact this will have on functionality:
sudo /sw/bin/python2.7 setup.py build install –home=$prefix –install-lib=$modules –install-scripts=$prefix –use-msgpackc=no
Thanks for sharing the msgpack switch.
Hi there,
Thanks for the install software – I was looking for a version of PyMol that still allowed me to ray trace!
I did come across an issue, though. When I tried to use the command « select chain a », I got a syntax error! I’m not sure how many commands have problems, but I was wondering if there is a reason and/or fix for this issue?
Thanks in advance for your help!
P.S. I installed the 64-bit version for my PC.
Trying to install pymol 2.1 under Ubuntu 16.04 LTS.
I installed all the dependencies according to your tutorial, and set the variables:
$ prefix=~/pymol-2.1
$ modules=$prefix/modules
But I get the following error which I don’t understand:
$ python setup.py build install –home=$prefix –install-lib=$modules –install-scripts=$prefix
Traceback (most recent call last):
File « setup.py », line 248, in
create_shadertext.create_all(generated_dir)
File « /home/mheller/Downloads/pymol/create_shadertext.py », line 25, in create_all
create_buildinfo(generated_dir, pymoldir)
File « /home/mheller/Downloads/pymol/create_shadertext.py », line 115, in create_buildinfo
»’ % (time.time(), sha, rev), file=out)
File « /home/mheller/Downloads/pymol/create_shadertext.py », line 55, in __exit__
self.close()
File « /home/mheller/Downloads/pymol/create_shadertext.py », line 47, in close
self.out = open(self.filename, « w »)
PermissionError: [Errno 13] Permission denied: ‘build/generated/PyMOLBuildInfo.h’
Exception ignored in: <bound method openw.__del__ of >
Traceback (most recent call last):
File « /home/mheller/Downloads/pymol/create_shadertext.py », line 57, in __del__
self.close()
File « /home/mheller/Downloads/pymol/create_shadertext.py », line 47, in close
self.out = open(self.filename, « w »)
PermissionError: [Errno 13] Permission denied: ‘build/generated/PyMOLBuildInfo.h’
Hi!
I didn’t test it on Linux yet (I have to reinstall my virtual machine), but it seems that either you don’t have enough acces on the files. Did you extract the archive with a sudo command or with another user?
If you are sudo, try to add « sudo » before « python …. », and if you have downloaded the archive as another user, try to do it again with your session.
Try maybe in the pymol source folder « chmod -R 755 . »
I can happily report that this was indeed a permissions issue.
Adding « sudo » before the « python » command did the trick! I kinda should have figured that out myself, but anyway: thank you very much, Thibault!!!
Hi there, thanks for the tutorial.
I just wanted to point out that whereas the linux version does run the setup.py file and compiles pymol, the windows tutorial does not. The windows tutorial takes a precompiled packaged 1.8.2 and simply moves the binaries around. So the c plus plus files in the package are not recompiled at all, which is why these instruction are not « compiling instructions » but installation instructions.
Hope this helps. Cheers, Mat