Prevent MacPyMOL from registering as a valid pdb/pml/etc viewer.
Hi phenix developers I just installed 1.7.3-928. Apparently, OS X thinks the internally distributed pymol is my preferred pdb viewer (as opposed to my more recent build in /Applications). This may have something to do with the Info.plist registering document types. A small change in Finder for the user, but it was quite maddening to figure out why I had opened a pdb and pseudoatom was not working. Can future builds keep the internally distributed pymol as walled in as possible? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
On Mon, Dec 19, 2011 at 10:24 AM, Francis E Reyes
I just installed 1.7.3-928. Apparently, OS X thinks the internally distributed pymol is my preferred pdb viewer (as opposed to my more recent build in /Applications). This may have something to do with the Info.plist registering document types. A small change in Finder for the user, but it was quite maddening to figure out why I had opened a pdb and pseudoatom was not working.
Can future builds keep the internally distributed pymol as walled in as possible?
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. (Apple's support for their installer tools is nearly nonexistent, presumably because distributing software this way doesn't allow them to skim off a 30% cut of the sale price.) So, I'll see what I can do, but it may be a "feature" that is difficult to disable. 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. -Nat
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. F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
On Mon, Dec 19, 2011 at 10:57 AM, Francis E Reyes
I used the command line installer. ( I put phenix in strange places ).
Okay, weird...
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)
I'm pretty confident this won't work - the actual MacPyMOL binary object is only about a third of the contents of the app bundle.
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?
Nope, Warren made the 0.99 builds freely available without purchasing a license - this is the only version of MacPyMOL that we are legally allowed to distribute (and this has been true for many years now). As far as I know the license terms have not changed significantly; at any rate, it is still easy to obtain and compile the current open-source PyMOL. But we don't distribute that because it requires X11, and the native MacPyMOL has always been proprietary.
Anyways I would welcome a slimmed version of phenix that didn't include PyMOL. My SSD would be much happier.
Actually, it's only 33MB out of about 1.8GB - for what it's worth, these are the largest sub-directories in 1.7.3 (with sizes in MB): 443 phenix-1.7.3-928/build 412 phenix-1.7.3-928/chem_data 197 phenix-1.7.3-928/phenix_regression 161 phenix-1.7.3-928/solve_resolve 149 phenix-1.7.3-928/phenix_examples 103 phenix-1.7.3-928/boost They're not going to get much smaller, unfortunately. :( -Nat
participants (2)
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Francis E Reyes -
Nathaniel Echols