Re: [COOT] Updating coot on Mac OS X 10.4

Eleanor Dodson Wed, 03 Dec 2008 02:47:00 -0800

coot still gives this message when attempting SSM superpose


Can make graph of .......

Eleanor


Michele Cianci wrote:

Hi Volks,

thanks for this discussion. It helped me in finding coot 0.5 for 10.4 and 
installing it.
However the last step described below was not quite the last one to make coot 
running (at least for me).
Running command line launching /Applications/coot.app/Contents/MacOS/coot
would give me the error message:
---------------------------------------------------
...

~/.coot-preferences/coot-preferences.scm:5:1: In expression 
(set-file-chooser-selector 0):
~/.coot-preferences/coot-preferences.scm:5:1: Unbound variable: 
set-file-chooser-selector
coot-exe: "/Applications/coot.app/Contents/MacOS/../coot/bin/coot"

coot-version:/Applications/coot.app/Contents/MacOS/../coot/bin/coot

core: #f
No core file found.  No debugging
---------------------------------------------------

So I tried to delete ~/.coot-preferences/coot-preferences.scmand that finally worked.

HTH,

mkl





________________________________
Da: Abhinav Kumar <[EMAIL PROTECTED]>
A: [email protected]
Inviato: Venerdì 21 novembre 2008, 3:10:55
Oggetto: Re: Updating coot on Mac OS X 10.4

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/cootthat runs a setup script that sets the environmentCharles



________________________________

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 CRYSTALLOGRAPHY60: 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
==========================================================================

ThanksAbhinavStanford Synchrotron Radiation LaboratoryJoint Center for Structural GenomicsMail Stop 99Phone: (650) 926-2992Fax: (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 forupdating coot to 0.5 version.

Is there some way of doing it. I have had problems using fink toupdate it.

Re: [COOT] Updating coot on Mac OS X 10.4

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