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

Nathaniel Echols nechols at lbl.gov
Thu May 27 11:50:17 PDT 2010

On Thu, May 27, 2010 at 11:32 AM, Ben Eisenbraun
<bene at hkl.hms.harvard.edu>wrote:

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

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