Re: [phenixbb] "Open in Coot" not working on 1.6.1-357

I am also having some similar issues, and pressing the Open in Coot, grays out the button, but does nothing. I have phenix installed with ./install on a Mac. I have coot 0.6.2-pre-1 (revision 2965) [with guile 1.8.6 embedded] [with python 2.6.5 embedded] and I have tried this in phenix 357. Even clicking the Coot button on Phenix Home window does nothing. The coot log window shows nothing. Sidenote: Open in Pymol does not work when opening from phenix, It gives some kind of error in phenix. I think "Open in Coot" was working previously, but I haven't found the problem. Daniel On Thu, May 27, 2010 at 1:50 PM, Nathaniel Echols wrote:

On Thu, May 27, 2010 at 11:32 AM, Ben Eisenbraun

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wrote:

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On Thu, May 27, 2010 at 12:31:41AM -0400, Ben Eisenbraun wrote:

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I can't seem to get the "Open in Coot" option to work in PHENIX. I tested version 1.6.1-357 on 32 and 64-bit linux as well as the OS X Intel version, and while Coot will open, it won't display the working data.

Could this be a gtk issue of some sort?

The first thing to check is whether Coot has Python embedded ("coot --version"). If you downloaded the package(s) from Paul's website, they need to have "python" in the package name, otherwise they won't work. The only time I've seen GTK-related issues is (inconsistently) in the standalone packages on Bill Scott's webpage, and the result was that even the buttons wouldn't appear.

Does PHENIX produce some sort of log of GUI events, stderr, whatnot? Is

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there a debugging mode that would output more information?

Yes: Utilities menu->Coot console log. Also, if you start the GUI with "--debug", all of the Coot output will be dumped to the console (and some other Phenix-specific debugging messages, but you can ignore those). This should indicate what is going wrong on the Mac version. (Which program are you running, by the way? Because the programs in Phenix all generate slightly different output, I have to write a separate function for each one for Coot, and PyMOL. . . not fun to maintain.) One other thing to try on Mac: open any program, load a PDB file, right-click on the magnifying glass icon next to the file, and select "Open in Coot". If this doesn't work, something weird is going on.

-Nat

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