Question: Pymol fails to run on Mac
0
gravatar for Reyhaneh
3.5 years ago by
Reyhaneh480
United Kingdom
Reyhaneh480 wrote:

Hi,

 

I have installed pymol on my Mac using:

brew install homebrew/science/pymol

when I try to run pymol I get the following error:

MP02s-iMac:$ pymol

Traceback (most recent call last):

  File "/usr/local/Cellar/pymol/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 71, in <module>

    import pymol
  File "/usr/local/Cellar/pymol/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 521, in <module>

    import pymol._cmd
ImportError: dlopen(/usr/local/Cellar/pymol/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/_cmd.so, 2): Library not loaded: /usr/local/lib/libGLEW.1.12.0.dylib

  Referenced from: /usr/local/Cellar/pymol/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/_cmd.so

 Reason: image not found

 

It seems I have two installation of python.

MPMAC02s-iMac:Downloads rey$ which python
/usr/local/bin/python

and 

MPMAC02s-iMac:Downloads rey$ type -a python
python is /usr/local/bin/python
python is /usr/bin/python

 

Do you know what might be causing the problem? Setting PYMOL_PATH didn't help either.

 

Thanks

pymol python mac • 2.2k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 3.5 years ago by Reyhaneh480
1

This commit is addressing this issue. I think it should be patched up already, run
brew update

brew doctor

ADD REPLYlink written 3.5 years ago by Sukhdeep Singh9.8k

I'm seeing a weird error as well - mine is with libpng, it's loading the wrong version even when I set the DYLIB_PATH variable. I'd suggest using EduPymol's DMG for Mac.

EDIT: Solution found - I just needed to update XQuartz. XQuartz is X11 - I had no idea that was the case. If brew doctor had been telling me X11 needed an update (instead of XQuartz needs an update), I'd have done it immediately.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by RamRS23k
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