Therein lies the problem (or at least A problem)....
COOT_PYTHON_DIR shouldn't be set (by you).
Instead, issue
source /sw/bin/init.sh
(or source /sw/bin/init.csh )
and then issue simply the command
coot
and see if it works?
On Sep 9, 2009, at 8:06 AM, Engin Ozkan wrote:
This is what I get.
[engin-ozkans-macbook-pro:~] eozkan% COOT_PYTHON_DIR was defined to
be /sw/share/coot/python
but no PyGtk and hence no coot_gui.
Entry contents: help()
Running string: help()
Welcome to Python 2.6! This is the online help utility.
Engin
On 9/9/09 7:25 AM, William G. Scott wrote:
I'm going to make a wild guess and suggest it is a python version
mismatch.
If you open the python scripting window and type in
help()
what do you see in the console window?
I get this:
BL INFO:: command input is: help()
Welcome to Python 2.6! This is the online help utility.
On Sep 8, 2009, at 10:47 AM, Engin Ozkan wrote:
Hi everybody,
Using the revision 2283 on 10.5, I am seeing this whenever I am
closing the application:
/sw/bin/coot: line 5: 19785 Segmentation fault /sw/bin/coot-
real "$@"
Yep, coot shuts down with a segmentation fault. I haven't tested
most functionality and it has not affected my use of coot yet, but
I assumed it might help to report it. This seems to be the same
bug observed by Christian on a 10.4 machine, because I get the
similar Preferences crash. Empty 0-coot.state.scm is also probably
due to the crash during exiting.
Engin
On 9/8/09 7:14 AM, William G. Scott wrote:
Hi Christian:
I just committed coot 0.6-pre-1-revision-2283 to fink cvs. It
fixes a bug on 64-bit where the menu would freeze when
superposition is invoked. I suppose there is a 0.0000001 chance
that it fixes the other problem too. I have no way to test on
10.5 intel (I still have 10.6) and haven't had direct access to
10.4 for a long time. This could be a problem with coot or with
one of many of its ca. 230 dependencies.
From what I have read, you can upgrade directly to SL (US $30, UK
£25), despite the propaganda on the box. I have ccp4 and coot and
the other crystallographic fink things running all in 64-bit now.
I'm hoping these will now pass the 70S ribosome test.
I hope this works in the meantime.
Bill
On Sep 8, 2009, at 5:08 AM, Christian Benda wrote:
Dear all,
we have updated coot to 0.6-pre-1 revision 2264 using fink on
our Macs running 10.4.11
to be able to use zalman stereo.
Unfortunately it seems like this coot or the combination is not
working correctly. So far,
there are two main issues:
1. coot freezes and closes down after selecting e.g. the
preferences menue
2. coot writes an empty 0-coot.state.scm file no matter what's
loaded into coot.
Any hints to what we can do? We really need the stereo and
therefore revision 2225 or
higher
Many thanks in advance
Christian
Dr. Christian Benda
Max Planck Institute of Biochemistry
Structural Cell Biology
Am Klopferspitz 18
D-82152 Martinsried
Germany
Phone: +49 (0)89 85 78 23 37
Fax: +49 (0)89 85 78 22 19
Email: be...@biochem.mpg.de
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111