May 14, 2009 - Its PyMOL is a free Open Source molecular viewing engine, rendering tool, and editor that can visualize 3D molecular structure down to the.

I would like to install PyMOL on my PC. I un-installed it yesterday because I previously installed python 2.7.9 via Python(x,y) while my PyMOL installation (which I installed months ago so I'm afraid I forgot how I did so) was using python 2.7.8 and the result was that PyMOL was no longer working properly, e.g., look at this screenshot I took, the GUI molecule viewer wasn't visible, just the console. I have tried using wheels files (namely amd64 version) but I have encountered pip problems. See the pip I have came along with my 64-bit Python 2.7.9 installation and the exe file for pip is called pip2.exe. So I changed the system environment variable PYTHONPATH to C: Python27 (where the python installation is) and PATH to C: Python27 Scripts which is where pip2.exe is (along with pip2.7.exe, easy_install.exe and easy_install-2.7.exe, if relevant).

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 from the Laboratory for Fluorescence Dynamics, University of California for the precompiled version of pymol available on his website () For 64 bits (1.8.2.0): • Download and install Python 2.7.9 (and only python 2.7.9) • 64 bits Computers: • The compilation may fail if you don’t have Virtual C++ compilator for Python: • You will need the precompiled version of pymol made. 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.

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. 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 () or () 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. 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.

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 🙂. 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. Blacklist 2011 scripts pdf free. I hope it can help you 🙂 Thibault. Hello Thibault, Thank you for the wonderful tutorial.