The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Some older Macs seem to crash with stereo graphics. If this happens to you, a workaround is to launch PyMOL explicitly in Mono mode with `pymol -M`. You can also set up an alias in your /.profile: alias pymol='pymol -M' See Also. Contact us to recommend an addition to our catalog, visit the Software Download site to see other listings, or review our list of software and technology tools that requires ordering. View Available Software. Download PyMOL for Mac OS X 10.8 or above Download PyMOL for Mac alternative X11-only build (OS X 10.9 or above) Note: X11 is a standard framework for creating applications with a graphical user interface on Unix-like operating system.
| Python-based Hierarchical ENvironment for Integrated Xtallography |
Instructions for installing external software interfacing with PHENIX
Coot
Coot is the standard programfor model-building into density, written chiefly by Paul Emsley. Theextensions included with the PHENIX GUIallow control of Coot from PHENIX, including automatic loading of models andmaps. This requires a build of Coot that includes a working Pythoninterpreter; if the PHENIX extensions are not functioning, this is almostcertainly due to the lack of Python in the Coot build. Note: the installersavailable on the CCP4 web page have not worked with PHENIX in the past; asof May 2011, the Mac installer appears to be fine, but you will need to specifythe path (/Applications/coot.app) in the PHENIX preferences.
Download mac migration assistant. Apple Windows Migration Assistant for Mac downloads as an EXE file and you'll need to install it on the PC you want to grab files from. Even though the app is around 5MB in size, the download took. Download Apple Migration Assistant for Mac to fix an issue with the Migration Assistant application in Mac OS X Snow Leopard.
- For Linux:
We recommend downloading installers directly fromPaulEmsley's web page. Any file with 'python' in the name is suitable for usewith PHENIX. Most of these will work on other OSes than those named, but wehaven't tested them extensively. - For Mac:
Two options are available: use the Finkpackage manager, or download a standalone installation. Both aredescribed on Bill Scott's web page. Note that you will need to berunning Snow Leopard (OS 10.6) to use many of these, but some obsolete (butstill functional) builds of Coot for older OSes are available. The builds arenow nightly, and include both command-line and graphical installers. For older versions ofMac OS (10.4 or 10.5), the more recent packages do not work with PHENIX, soyou will need to use the obsoleteCoot 0.6 build.
Pymol Free Download
To run Coot from the PHENIX GUI, you will either need to have the 'coot'executable somewhere in your shell's searchpath, or enter it inPreferences->Graphics->Full path to Coot. A few specific paths are searchedautomatically. On Mac, most installations should be automatically detected,but you may need to set the path explicitly to ensure that the correct versionis used.
PyMOL
PyMOL is a popular open-source moleculargraphics program, written by the late Warren DeLano and now maintained bySchrodinger. We distribute anobsolete binary build of PyMOL (version 0.99) with PHENIX, but this islacking some significant features and we recommend that you use the newestrelease. A variety of options are available for both Linux and Mac, includinginstallation via some package managers (Fink, and some Linux distributions),custom installation from source, or proprietary builds (with additionalfeatures) purchased from Schrodinger. Either open-source or proprietaryversions should work well with PHENIX. (We mostly test with MacPyMOL version1.2.)
The fink pymol package is already preconfigured to do the right thing to use apbs as a plugin. Some older Macs seem to crash with stereo graphics. If this happens to you, a workaround is to launch PyMOL explicitly in Mono mode with `pymol -M`. You can also set up an alias in your /.profile: alias pymol='pymol -M' See Also. Contact us to recommend an addition to our catalog, visit the Software Download site to see other listings, or review our list of software and technology tools that requires ordering. View Available Software. Download PyMOL for Mac OS X 10.8 or above Download PyMOL for Mac alternative X11-only build (OS X 10.9 or above) Note: X11 is a standard framework for creating applications with a graphical user interface on Unix-like operating system.
| Python-based Hierarchical ENvironment for Integrated Xtallography |
Instructions for installing external software interfacing with PHENIX
Coot
Coot is the standard programfor model-building into density, written chiefly by Paul Emsley. Theextensions included with the PHENIX GUIallow control of Coot from PHENIX, including automatic loading of models andmaps. This requires a build of Coot that includes a working Pythoninterpreter; if the PHENIX extensions are not functioning, this is almostcertainly due to the lack of Python in the Coot build. Note: the installersavailable on the CCP4 web page have not worked with PHENIX in the past; asof May 2011, the Mac installer appears to be fine, but you will need to specifythe path (/Applications/coot.app) in the PHENIX preferences.
Download mac migration assistant. Apple Windows Migration Assistant for Mac downloads as an EXE file and you'll need to install it on the PC you want to grab files from. Even though the app is around 5MB in size, the download took. Download Apple Migration Assistant for Mac to fix an issue with the Migration Assistant application in Mac OS X Snow Leopard.
- For Linux:
We recommend downloading installers directly fromPaulEmsley's web page. Any file with 'python' in the name is suitable for usewith PHENIX. Most of these will work on other OSes than those named, but wehaven't tested them extensively. - For Mac:
Two options are available: use the Finkpackage manager, or download a standalone installation. Both aredescribed on Bill Scott's web page. Note that you will need to berunning Snow Leopard (OS 10.6) to use many of these, but some obsolete (butstill functional) builds of Coot for older OSes are available. The builds arenow nightly, and include both command-line and graphical installers. For older versions ofMac OS (10.4 or 10.5), the more recent packages do not work with PHENIX, soyou will need to use the obsoleteCoot 0.6 build.
Pymol Free Download
To run Coot from the PHENIX GUI, you will either need to have the 'coot'executable somewhere in your shell's searchpath, or enter it inPreferences->Graphics->Full path to Coot. A few specific paths are searchedautomatically. On Mac, most installations should be automatically detected,but you may need to set the path explicitly to ensure that the correct versionis used.
PyMOL
PyMOL is a popular open-source moleculargraphics program, written by the late Warren DeLano and now maintained bySchrodinger. We distribute anobsolete binary build of PyMOL (version 0.99) with PHENIX, but this islacking some significant features and we recommend that you use the newestrelease. A variety of options are available for both Linux and Mac, includinginstallation via some package managers (Fink, and some Linux distributions),custom installation from source, or proprietary builds (with additionalfeatures) purchased from Schrodinger. Either open-source or proprietaryversions should work well with PHENIX. (We mostly test with MacPyMOL version1.2.)
Pymol Mac Free
As with Coot, you may have to point PHENIX to the PyMOL executable (inPreferences->Graphics->Full path to PyMOL) if it is not found automatically.On Mac, it will use /Applications/MacPyMOL.app if present.
