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

RaDaniel Christian 성준 rendereason at gmail.com
Tue Jun 8 15:19:33 PDT 2010

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

On Thu, May 27, 2010 at 1:50 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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.
> -Nat
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