2020. 2. 10. 01:18ㆍ카테고리 없음
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):.
The best performance was obtained using the Intel compiler + Intel MKL under. To use SPAMS with matlab R2011a and later, do not forget to run the. For MacOS X (because OpenMP is not supported by the compiler clang at the moment). Intel® Math Kernel Library for Mac OS* X User's Guide Intel® MKL - Mac OS* X Document Number: 315932-023US Legal Information. To refresh your terminal. Now, check that these environment variables are set up correctly: MKLROOT /opt/intel//compilers_and_libraries_2016.2.146/mac/mkl.
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 « installpymol.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 Pymolwin32). If i click directly on the installpymol.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 »protein000.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 raytraceframes=1 », That’s what I do.
I hope it can help you 🙂 Thibault. 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. 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? 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: PyMOLinstallationC: Python27 Scripts pip.exe install numpy-1.9.3+mkl-cp27-none-winamd64.whl numpy-1.9.3+mkl-cp27-none-winamd64.whl is not a supported wheel on this platform. C: PyMOLinstallationecho Pymol lib installation Pymol lib installation C: PyMOLinstallationC: Python27 Scripts pip.exe install pymol-1.8.0.0-cp27-none-winamd64.whl pymol-1.8.0.0-cp27-none-winamd64.whl is not a supported wheel on this platform.
C: PyMOLinstallationecho PWN Graphic interface installation PWN Graphic interface installation C: PyMOLinstallationC: Python27 Scripts pip.exe install pymollauncher-1.0-cp27-none-winamd64.whl pymollauncher-1.0-cp27-none-winamd64.whl is not a supported wheel on this platform. Can someone help me with the MAC? I’ve installed fink, xquartz, and am running 10.11. Appreciate your reply, but I can not figure it out. I don’t think there is a hidden ` in the code I pasted.
Mkl Not Supported For Mac Mac
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:). Hello, I am working to install the open-source PyMOL 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.
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! 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 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): Pmw2.0.0 from file:///C:/Python27/Pymolwin32-rute/Pymolwin32/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 pymollauncher-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. 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 installpymol.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 Pymolecho C: Python27 pymol.exe C: Python27 pymol.exe C: Python27 Pymolpause Press any key to continue so what do i do now exactly? Thank you in advance!
Hello, trying to install PyMOL on Windows10 here – I downloaded and installed python-2.7.9.amd64.msi – I checked the registry on HKEYLOCALMACHINE 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-winamd64.whl?
What could be wrong? Thank you so much Javier. Error C: Pymolwin64 Pymolwin64installpymol.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. 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/mmtfparser.cpp:31: contrib/mmtf-c/mmtfparserprivate.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? 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. Trying to install pymol 2.1 under Ubuntu 16.04 LTS.