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

Ben Eisenbraun bene at hkl.hms.harvard.edu
Mon Jun 14 12:20:33 PDT 2010

Hi Nat,

> The first thing to check is whether Coot has Python embedded ("coot
> --version").

I knew about this one:

/programs/l/coot/0.6.2-pre-1-r2969/bin/coot-real --version
0.6.2-pre-1 (revision 2969)  [with guile 1.8.7 embedded] [with python 2.6.0 embedded]

> 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

Ah, that's handy.

So first off I see that I somehow got an older version of Coot lodged in my
~/.phenix/prefs.params file.  It was pointing to a linux Coot 0.6.1 32-bit
installation.  I assume that will override the phenix.find_coot_command?

Once I removed that, I can get our 64-bit installations of PHENIX and Coot
to cooperate.  On the 64-bit version I see:

Coot: Running python script /programs/i386-linux/phenix/1.6.2-432/phenix-1.6.2-432/phenix/wxGUI2/Coot.py
Coot: Loading PHENIX Coot extensions. . .
Coot: xml-rpc server running on port 46712

And then the coot output as it reads the data files.  On the 32-bit version
I see:

Coot: Running python script /programs/i386-linux/phenix/1.6.2-432/phenix-1.6.2-432/phenix/wxGUI2/Coot.py
Coot: (use-graphics-interface-state)

And the buttons and molecule are not loaded.

I built the 32-bit Coot on CentOS 4 and the 64-bit Coot on CentOS 5.
They're both using the autobuilder script with identical arguments, but
using Paul's 32-bit CentOS build works fine, so there's definitely
something gone amuck in our 32-bit build.

The Mac problems appear to have cleared up when I removed the hard-coded
path to the linux version of Coot in my preferences file.

So everything's working as expected now.  Thanks for your assistance.


| Ben Eisenbraun                              | Software Sysadmin      |
| Structural Biology Grid                     | http://sbgrid.org      |
| Harvard Medical School                      | http://hms.harvard.edu |

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