Only the GUI, as far as I know - although apparently there are problems with the version of Python we're currently distributing, but I don't think those will affect most people. -Nat On Fri, Oct 25, 2013 at 7:37 AM, Bosch, Juergen wrote:

is this warning only for the GUI or also the CLI ? Thanks,

Jürgen

On Oct 25, 2013, at 10:22 AM, Nathaniel Echols wrote:

There is some kind of strange issue with wxPython on the new Mac OS ("Mavericks"), which for at least the 1.8.4 version prevents Phenix application windows (but not the main GUI) from opening. It is also printing out an extraordinary number of warning messages about fonts to the console. I'm hoping there is a simple solution (which seems likely, since 1.8.2 is mostly okay despite using the same version of wxPython), but until we figure out what is causing this, I recommend leaving your Macs unmolested if you want to use the Phenix GUI.

Updates to follow if-and-when I fix this.

thanks, Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu

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But, no, that problem existed before the Mavericks update (with Snow Leopard and Mountain Lion). I had learned to live with it. Engin On 10/25/13 1:45 PM, Petri Kursula wrote:

What I saw were problems with phenix.refine (well-did not try anything else yet). The job seems to start normally (no error messages), but when you check the log file, nothing is happening (it remains empty or stops at initial steps). If you abort, close Phenix and restart it, the exactly same job runs just fine. I'm starting Phenix GUI from 'Applications', not command line.

Petri

--- Petri Kursula, PhD project leader, adjunct professor Department of Biochemistry & Biocenter Oulu, University of Oulu, Finland Department of Chemistry, University of Hamburg/DESY, Germany www.biochem.oulu.fi/kursula http://www.biochem.oulu.fi/kursula www.desy.de/~petri/research http://www.desy.de/%7Epetri/research [email protected] mailto:[email protected] ---

On 25 Oct 2013, at 17:01, Nathaniel Echols mailto:[email protected]> wrote:

...

Only the GUI, as far as I know - although apparently there are problems with the version of Python we're currently distributing, but I don't think those will affect most people.

-Nat

On Fri, Oct 25, 2013 at 7:37 AM, Bosch, Juergen mailto:[email protected]> wrote:

is this warning only for the GUI or also the CLI ? Thanks,

Jürgen

On Oct 25, 2013, at 10:22 AM, Nathaniel Echols wrote:

...

There is some kind of strange issue with wxPython on the new Mac OS ("Mavericks"), which for at least the 1.8.4 version prevents Phenix application windows (but not the main GUI) from opening. It is also printing out an extraordinary number of warning messages about fonts to the console. I'm hoping there is a simple solution (which seems likely, since 1.8.2 is mostly okay despite using the same version of wxPython), but until we figure out what is causing this, I recommend leaving your Macs unmolested if you want to use the Phenix GUI.

Updates to follow if-and-when I fix this.

thanks, Nat _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 tel:%2B1-410-614-4742 Lab: +1-410-614-4894 tel:%2B1-410-614-4894 Fax: +1-410-955-2926 tel:%2B1-410-955-2926 http://lupo.jhsph.edu http://lupo.jhsph.edu/

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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On Fri, Oct 25, 2013 at 11:45 AM, Petri Kursula wrote:

What I saw were problems with phenix.refine (well-did not try anything else yet). The job seems to start normally (no error messages), but when you check the log file, nothing is happening (it remains empty or stops at initial steps). If you abort, close Phenix and restart it, the exactly same job runs just fine. I’m starting Phenix GUI from ‘Applications’, not command line.

Can you either a) try starting on the command line (/Applications/PHENIX-1.8.4-1496/Contents/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/bin/phenix) and looking for console output, or b) open the Console app and see what is printed out? I suspect it will have an error message involving "malloc", because that's what happens to be sometimes. (Always with either phenix.refine or phenix.maps.) As far as I can tell this is some kind of very low-level error in either Python or the compiler used to build Phenix - as you note, it is not consistently reproducible either, and it doesn't seem to be correlated with any specific model or data issues that I can see. -Nat

If you don't want to allow all outside apps you can right-click/cmd and select open. That should allow it to run also. It's only for the first time it's ran too. Cheers, BM On 26 Oct 2013, at 10:35 am, "Nathaniel Echols" mailto:[email protected]> wrote: Following up on this: it is not quite so dire as I had originally thought, just horribly confusing (and still fundamentally broken). When you click an app icon after the GUI first comes up, it will move the main GUI to the background, and the menus will change to the menus for the specific app, but the app window doesn't actually appear. Clicking on the dock icon for the active GUI magically brings all windows to the foreground, and after that windows seem to appear normally. So it is ultimately usable, in theory. I will keep poking at this but I can't see anything wrong in our code, and the font-related error messages are certainly not going away easily. PS. Apple helpfully resets the security settings when you upgrade, so attempting to install a new version of Phenix is going to pop up an error about us not being a registered developer. You can un-break it by changing the security settings to allow apps from anywhere to be installed. I'll see if there's a solution to this that doesn't involve giving Apple 30% of our NIH grants. -Nat On Fri, Oct 25, 2013 at 7:22 AM, Nathaniel Echols mailto:[email protected]> wrote: There is some kind of strange issue with wxPython on the new Mac OS ("Mavericks"), which for at least the 1.8.4 version prevents Phenix application windows (but not the main GUI) from opening. It is also printing out an extraordinary number of warning messages about fonts to the console. I'm hoping there is a simple solution (which seems likely, since 1.8.2 is mostly okay despite using the same version of wxPython), but until we figure out what is causing this, I recommend leaving your Macs unmolested if you want to use the Phenix GUI. Updates to follow if-and-when I fix this. thanks, Nat _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb