[phenixbb] Prevent MacPyMOL from registering as a valid pdb/pml/etc viewer.

Francis E Reyes Francis.Reyes at Colorado.EDU
Mon Dec 19 10:57:37 PST 2011

On Dec 19, 2011, at 11:42 AM, Nathaniel Echols wrote:

> Which installer did you use?  I've found it extraordinarily difficult
> to keep OS X from doing various truly stupid things with the
> package-based installer - it took me several days just to figure out
> how to prevent it from overwriting Python installations elsewhere on
> the system.  

I used the command line installer. ( I put phenix in strange places ). 

>  So, I'll see
> what I can do, but it may be a "feature" that is difficult to disable.

Remove the bundle completely. i.e.  Why not pull MacPyMOL.app/Contents/MacOS/MacPyMOL out from the .app directory structure and distribute it as an executable underneath  a macpymol.noindex under phenix-1.7.1-743/build/mac-intel-osx-x86_64/base/bin.  (.noindex to disable spotlight indexing of this dir as well)

The calling functions will have to be rewritten to not rely on Finder to find it though.  (i.e. if you're using 'open', etc)

> Maybe it's time to stop distributing PyMOL with Phenix?  Version 0.99
> is quite obsolete at this point, and it's relatively easy to install.
> '

I thought that 0.99 was kept around for specific reasons (maybe something is missing/broken in future builds?)

Then again wasn't 0.99 the point at which Shroedinger took over and maybe changed the license terms?

Anyways I would welcome a slimmed version of phenix that didn't include PyMOL. My SSD would be much happier.


Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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