BS"D Dear Paul and Nat, The version of coot that is available from CCP4 is 0.6.2 (3562). This was shown on the CCP4 download page for Mac OSX, as one of the additional things you might want. The advantage of this precompiled binary is that is claims to be compatible back to 10.4.x. Aside from the problem that the program is looking for the geometry libraries in one place and they are located in another place (that is a CCP4 issue), I could not get Phenix (1.7.1-743) to communicate with Coot. I supplied the path to coot (/Applications/coot.app) and Phenix started coot, but could not load the refinement information. I tested this during a refinement run on a 10.5.x machine, and from the "Results" pane for a finished job under 10.6.8. In the latter case, pressing "Open in Coot" does fire up the program, but the molecule and maps are not loaded. On the other hand, choosing "Open in PyMOL" does indeed display the molecule and maps. Thanks Harry On Jul 26, 2011, at 9:47 PM, Nathaniel Echols wrote:

On Tue, Jul 26, 2011 at 5:35 AM, Harry Greenblatt wrote:

...

I see that CCP4 has a new version of coot for OSX that runs under X-windows. I'm not interested in using Fink, and Bill Scott's standalone binaries don't seem to work on my laptop, and we also have some machines at 10.5.x, and new versions of coot in that format are not available. But the CCP4 version wasn't built it to communicate with Phenix during a run. Is that functionality something that can be added easily post-facto?

I just installed this and tried for myself, and it appears to be working fine. The only problem I noticed is that the extension which allows us to modify the menubar and toolbar from a Python script is broken again, so you don't see the buttons for toggling the Phenix connection and hydrogen appearance. But the update during refinement is working as expected - what was your experience with it?

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

------------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology [email protected] Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

On Wed, Jul 27, 2011 at 7:05 AM, Ben Eisenbraun wrote:

...

The version of coot that is available from CCP4 is 0.6.2 (3562).  This was shown on the CCP4 download page for Mac OSX, as one of the additional things you might want.  The advantage of this precompiled binary is that is claims to be compatible back to 10.4.x.

There is a thread here with details on how to troubleshoot this sort of problem:

http://phenix-online.org/pipermail/phenixbb/2010-May/015207.html

Actually, this is now partially obsolete (sorry!). The Coot console output will always be the most useful in determining whether or not the programs will communicate - aside from the presence of Python, of course. I used to redirect the console output to an internal buffer in Phenix, but since this was causing freezes on some configurations, I now leave it alone. -Nat

On Tue, Jul 26, 2011 at 11:42 PM, Harry Greenblatt wrote:

    The version of coot that is available from CCP4 is 0.6.2 (3562).  This was shown on the CCP4 download page for Mac OSX, as one of the additional things you might want.  The advantage of this precompiled binary is that is claims to be compatible back to 10.4.x.

That's what I'm using - I can't rule out that something has changed since 1.7.1, however. The only change I'm aware of offhand is that it should now find /Applications/coot.app automatically (although given how unreliable that distribution has been, I'm not sure it's a good idea).

Aside from the problem that the program is looking for the geometry libraries in one place and they are located in another place (that is a CCP4 issue), I could not get Phenix (1.7.1-743) to communicate with Coot.  I supplied the path to coot (/Applications/coot.app) and Phenix started coot, but could not load the refinement information.  I tested this during a refinement run on a 10.5.x machine, and from the "Results" pane for a finished job under 10.6.8.  In the latter case, pressing "Open in Coot" does fire up the program, but the molecule and maps are not loaded.  On the other hand, choosing "Open in PyMOL" does indeed display the molecule and maps.

Okay, the way to test this is a little bit convoluted if you used the graphical installer - try this from the command line: source /Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix_env.sh phenix (if you're using tcsh, just remove ".sh" from the end of the source script) Then re-open your refinement results, click "Open in Coot", and send me the console output. On my computer it ends with this: Running python script /Users/nat/phenix/src/phenix/wxGUI2/Coot.py Could not import coot_python module! PHENIX GUI extensions will be disabled. Loading PHENIX Coot extensions... xml-rpc server running on port 40092 -Nat

BS"D Dear All, Following Nat's suggestion, I have recorded the console log and sent that to him. But for anybody else interested, here are the final lines of the output (partially shortened for clarity), and it seems that gtk can't be found: PHENIX-1.7.1-743 Running python script /Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/wxGUI2/Coot.py PHENIX-1.7.1-743 Traceback (most recent call last): PHENIX-1.7.1-743 File "<string>", line 1, in <module> PHENIX-1.7.1-743 File "/Applications/PHENIX-1.7.1-743/Contents/phenix-1.7.1-743/phenix/wxGUI2/Coot.py", line 24, in <module> PHENIX-1.7.1-743 import gtk PHENIX-1.7.1-743 ImportError: No module named gtk

Sorry for the multiple emails, but I just remembered that the procedure below is more trouble than necessary - if you launched Phenix from the icon, you can still get to the console by running Apple's Console.app, which is in /Applications/Utilities, or this command:

open -a Console

This should have all of the Coot output.

------------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology [email protected] Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

BS"D Dear Nat,

It may still be possible to make the connection with Phenix even if the GTK module is unavailable. So, a final experiment:

1. Start Coot 2. From the "Calculate" menu, select "Scripting"->"Python..." 3. Try typing each of these commands and see what happens: import gtk import gobject

Here is the result from the console log for the two commands (both fail): Entry contents: import gtk Running string: import gtk Traceback (most recent call last): File "<string>", line 1, in <module> ImportError: No module named gtk Entry contents: import gobject Running string: import gobject Traceback (most recent call last): File "<string>", line 1, in <module> ImportError: No module named gobject

The first command will almost certainly fail - I'm hoping that the second still works.

Thanks Harry ------------------------------------------------------------------------- Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology [email protected] Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel