[phenixbb] getting phenix and coot to talk on OSX

Harry Greenblatt Harry.Greenblatt at weizmann.ac.il
Tue Jul 26 23:42:35 PDT 2011


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.



On Jul 26, 2011, at 9:47 PM, Nathaniel Echols wrote:

> On Tue, Jul 26, 2011 at 5:35 AM, Harry Greenblatt
> <harry.greenblatt at weizmann.ac.il> 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
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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           harry.greenblatt at weizmann.ac.il
Weizmann Institute of Science        Phone:  972-8-934-3625
Rehovot, 76100                       Facsimile:   972-8-934-4159

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