[phenixbb] Coot failed to launch in Phenix after CCP4 update

Nathaniel Echols nechols at lbl.gov
Tue Jan 6 16:27:23 PST 2015

On Tue, Jan 6, 2015 at 4:01 PM, Shun Liu <sliu.xtal at gmail.com> wrote:

> It works! Thank you so much for this! I hope that in the future an
> installation package including all these softwares can be available for GUI
> users and when a new version of one software is available, what we need to
> do is only to click the mouse to update it. Thank you again.

Most of these programs are under restrictive licenses which limit their
distribution.  (Coot is the big exception, but it's also even messier to
build than Phenix.)  If you want an integrated solution, I urge you to look
into joining SBGrid, which takes care of all building/installation issues
and will automatically push out updates as they become available.  (This is
done on a per-lab basis but I have also seen individual laptops set up as
SBgrid clients.)  The disadvantages are (1) it costs money, and (2) it may
not always update as quickly as you'd like - looks like they haven't
switched to CCP4 6.5 yet but I assume this is what happens when you release
software right before Christmas.  But I think it is a huge improvement over
the old system where random grad students got stuck handling system
administration and arcane software.  It has certainly simplified Phenix
support, especially where Rosetta integration is concerned.

(In any case, I have modified the script that auto-detects Coot
installations so that it will also check for CCP4 installations on Mac -
and pick the newest one containing Coot - so you won't have to enter this
in the preferences any more.)

Just be glad you're doing crystallography and not next-gen sequencing -
programs like Phenix/CCP4/Coot are vastly simpler to install and use, and
there's much less fragmentation of developer efforts (especially since
everyone has standardized on Coot for interactive model-building).

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