Hi Charles,
This worked fine. Wonderful. Thanks so much.
I guess what was left unspecified was the path to the coot binary,
i.e. /Applications/coot.app/Contents/MacOS/coot
Iain, please try this out.
Thanks
Abhinav
Abhinav Kumar
JCSG @ SSRL, MS 99
2575 Sand Hill Road
Menlo Park, CA 945025-7015
Phone: 650 926 2992
Fax: 650 926 3292
On Nov 20, 2008, at 12:45 AM, Ballard, CC ((Charles)) wrote:
Hi
can you command line launch using
/Applications/coot.app/Contents/MacOS/coot
that runs a setup script that sets the environment
Charles
From: Abhinav Kumar [mailto:[EMAIL PROTECTED]
Sent: 19 November 2008 23:09
To: Ballard, CC (Charles)
Subject: Re: [COOT] Updating coot on Mac OS X 10.4
Thanks Charles.
Where do I find the crash log?
I didn't use a terminal to start coot, rather, used mouse to click
on coot icon in Application folder.
However, I also tried running coot from /Applications/coot.app/
Content/coot/bin/coot and got this:
========================================================
If have found this software to be useful, you are requested to
cite:
Coot: model-building tools for molecular graphics
Emsley P, Cowtan K
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
60: 2126-2132 Part 12 Sp. Iss. 1 DEC 2004
The reference for the REFMAC5 Dictionary is:
REFMAC5 dictionary: organization of prior chemical knowledge and
guidelines for its use
Vagin AA, Steiner RA, Lebedev AA, Potterton L, McNicholas S,
Long F, Murshudov GN
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
60: 2184-2195 Part 12 Sp. Iss. 1 DEC 2004
If using "SSM Superposition", please cite:
Secondary-structure matching (SSM), a new tool for fast
protein structure alignment in three dimensions
Krissinel E, Henrick K
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
60: 2256-2268 Part 12 Sp. Iss. 1 DEC 2004
Acquiring application resources from //Users/Shared/pac5/coot/
coot.app/Contents/coot/share/coot/cootrc
INFO:: splash_screen_pixmap_dir //Users/Shared/pac5/coot/coot.app/
Contents/coot/share/coot/pixmaps
** (coot:15026): WARNING **: Couldn't find pixmap file: coot-0.5.xpm
(coot:15026): GdkPixbuf-WARNING **: Cannot open pixbuf loader
module file '/Users/Shared/pac6/coot/coot.app/Contents/coot/etc/
gtk-2.0/gdk-pixbuf.loaders': No such file or directory
(coot:15026): GdkPixbuf-WARNING **: Error loading XPM image loader:
Image type 'xpm' is not supported
** ERROR **: Couldn't create replacement pixmap.
aborting...
Abort
======================================================================
====
Thanks
Abhinav
Stanford Synchrotron Radiation Laboratory
Joint Center for Structural Genomics
Mail Stop 99
Phone: (650) 926-2992
Fax: (650) 926-3292
Ballard, CC (Charles) wrote:
Hi Abhinav
I am responsible for the failed binary. Can you send me the crash
log
from console.app ? As soon as CCP4 6.1 is out of the door (possibly
even by this Friday) I will take a look at it.
Charles Ballard
CCP4
-----Original Message-----
From: Mailing list for users of COOT Crystallographic Software
[mailto:[EMAIL PROTECTED] On Behalf Of Abhinav Kumar
Sent: 19 November 2008 20:04
To: [email protected]
Subject: Re: [COOT] Updating coot on Mac OS X 10.4
Thanks Iain.
I downloaded the package and it installed without any problem.
However, when I click on it to start, it pop ups the starting logo
and
then disappears.
Thanks
Abhinav
Stanford Synchrotron Radiation Laboratory Joint Center for Structural
Genomics Mail Stop 99
Phone: (650) 926-2992
Fax: (650) 926-3292
Iain Kerr wrote:
I was pointed to a universal installer here:
http://www.ccp4.ac.uk/download/os.php
Didn't work for me though..perhaps it will work on your system.
HTH,
Iain
Abhinav Kumar wrote:
Hi Paul and Bill,
I have a Mac OS X 10.4 (tiger).
I wanted to update coot to the latest version.
Since Bill's old machine (10.4) died, there is no instruction for
updating coot to 0.5 version.
Is there some way of doing it. I have had problems using fink to
update it.
