Re: [COOT] error loading pixmap file

[Charles Ballard]

Hi

Assuming this is the GTK2 hardwiring of loader locations.

Can you locate your gdk-pixbuf.loaders file (mine is under $COOT/etc/ 
gtk-2.0) and check that the loaders for png and svg are defined, then  
confirm that they are where this file would indicate them to be.


If all looks correct then you can force that these file be used using  
thus (relocation can cause problems),  the GDK pixmap module file  
location can be overriden by the GDK_PIXBUF_MODULE_FILE environment  
variable (what I use is below)


GDK_PIXBUF_MODULE_FILE=$COOT_PREFIX/etc/gtk-2.0/gdk-pixbuf.loaders

although version numbers may have to change, as may location of  
libraries.


If the locations are not as in the loader file then you will have to  
regenerate the loader using


gdk-pixbuf-query-loaders

piping the output to a file and replacing gdk-pixbuf.loaders with  
it.  Before doing this you have to  set (use a hardwired path) to  
point to the loaders themselves


GDK_PIXBUF_MODULEDIR=$COOT_PREFIX/lib/gtk-2.0/2.10.0/loaders

Charles

On 7 May 2009, at 22:40, Alejandro Buschiazzo wrote:


Hi,

I just upgraded coot to 0.6 (pre-1 revision 1941) on my Intel MacOS  
X (10.4.11).


It launches, but gives a long list of errors, couldn't find any  
workaround following Bill

Scott's page, coot's FAQ, etc.

The errors start right away starting with :

 ** (coot-real:2487): WARNING **: Error loading pixmap file: /usr/ 
local/xtal/coot

/share/coot/pixmaps/display-manager.png 

...and then a bunch of

 Error loading icon: Couldn't recognize the image file format for  
file '/usr/loca

l/xtal/coot/share/coot/pixmaps/add-alt-conf.svg' ... 

Also a few of these at the end :

 (coot-real:2487): Gtk-WARNING **: Error loading icon: Couldn't  
recognize the ima
ge file format for file '/usr/local/xtal/coot/share/themes/Glossy_P/ 
gtk-2.0/stoc

k_zoom_fit_width.png ...

It still works, but the windows, buttons and general appearance are  
really looking quite
bad (or even absent); annoyingly enough, each molecule being loaded  
again triggers a

long list of warnings of the kind:

 ** (coot-real:2487): WARNING **: Pixbuf theme: Cannot load pixmap  
file /usr/loca
l/xtal/coot/share/themes/Glossy_P/gtk-2.0/button_round.png:  
Couldn't recognize t
he image file format for file '/usr/local/xtal/coot/share/themes/ 
Glossy_P/gtk-2.

0/button_round.png'


** (coot-real:2487): WARNING **: Invalid borders specified for  
theme pixmap:
/usr/local/xtal/coot/share/themes/Glossy_P/gtk-2.0/ 
button_round.png,

borders don't fit within the image 

Any help will be very much appreciated!!

[COOT] modified Asp link to mainchain

[Christian Roth]

Dear all,

it seems to be that I have a modified Asp in my structure. It seems that the 
side chain reacted with the main chain to an imide. I deleted the 
coorespondign O from the side chain and modified the pdb in the way that I 
added a link description between CG of Asp and N of following Gly residue. It 
seems to be O.K. during refinement and I can refine the Asp residue alone 
without a breakage of the CG-N bond. However when I try to refine it with the 
neighbouring residues the CG-N bond breaks. I could also add the SNN Monomer 
at this position but than my chain is not longer continous, but this is 
definitely the case. How I have to modify my pdb that the an refeinemnt over 
more residues is possible?

Thanks for your help

Christian  
-- 
Christian Roth
Institut für Bioanalytische Chemie
Biotechnologisch-Biomedizinisches Zentrum
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Telefon: +49 (0)341 97 31316
Fax: +49 (0)341 97 31319

[COOT] subversion build on ubuntu 9.04 fails : [: =: unary operator expected error

[hari jayaram]

Hi ..I tried a coot subversion (revision 1994) built-it-simple python on the
newest ubuntu 9.04

The build crashes just after it builds guile and ( 16-coot.txt in the build
directory ) reads :

checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... no
configure: error: guile required but not found
./build-it-gtk2-simple: line 2742: [: =: unary operator expected
NO need to update libtool
/home/hari/autobuild/ex-charlie_2009-05-08__T20_14_49/coot-0.6-pre-1
make: *** No targets specified and no makefile found.  Stop.

This happens only on the new ubuntu (on a 32 bit 9.04 system) .
I was able to build this revision without any problem on Ubuntu 8.04 64 bit

Just thought I would write in , in case anybody was seeing the same problem
or has a solution
SOme of the other stuff also  spooled to screen before the failure to build
is pasted below:

Thanks for your help
Hari

--2009-05-08 16:14:52--
http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile/guile-1.8.5.tar.gz
Resolving www.mirrorservice.org... 212.219.56.133, 212.219.56.134,
212.219.56.138, ...
Connecting to www.mirrorservice.org|212.219.56.133|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3933369 (3.8M) [application/x-gzip]
Server file no newer than local file
`/home/hari/autobuild//sources/guile-1.8.5.tar.gz' -- not retrieving.

./build-it-gtk2-simple: line 2395: 127: command not found
--2009-05-08 16:16:05--
http://www.ysbl.york.ac.uk/~emsley/software/extras/net-http-0.3.1.tar.gz
Resolving www.ysbl.york.ac.uk... 144.32.72.243
Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 26907 (26K) [application/x-gzip]
Server file no newer than local file
`/home/hari/autobuild//sources/net-http-0.3.1.tar.gz' -- not retrieving.

configure: warning: cannot execute guile-config
configure: warning: cannot execute NONE-guile-config
configure: warning: cannot execute NONE-guile-config
./configure: 580: is: not found
sed: can't read Makefile: No such file or directory
make: *** No rule to make target `install'.  Stop.
--2009-05-08 16:16:08--
http://www.ysbl.york.ac.uk/~emsley/software/extras/greg-2.0.0-pe.tar.gz
Resolving www.ysbl.york.ac.uk... 144.32.72.243
Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 453770 (443K) [application/x-gzip]
Server file no newer than local file
`/home/hari/autobuild//sources/greg-2.0.0-pe.tar.gz' -- not retrieving.

--2009-05-08 16:16:17--
http://www.mirrorservice.org/sites/ftp.gnu.org/gnu/guile-gtk/guile-gtk-2.1.tar.gz
Resolving www.mirrorservice.org... 212.219.56.138, 212.219.56.139,
212.219.56.153, ...
Connecting to www.mirrorservice.org|212.219.56.138|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 781985 (764K) [application/x-gzip]
Server file no newer than local file
`/home/hari/autobuild//sources/guile-gtk-2.1.tar.gz' -- not retrieving.

--2009-05-08 16:16:23--
http://www.ysbl.york.ac.uk/~emsley/software/extras/guile-gui-0.2.tar.gz
Resolving www.ysbl.york.ac.uk... 144.32.72.243
Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 33885 (33K) [application/x-gzip]
Server file no newer than local file
`/home/hari/autobuild//sources/guile-gui-0.2.tar.gz' -- not retrieving.

--2009-05-08 16:16:24--
http://www.ysbl.york.ac.uk/~emsley/software/extras/neil-jerram.guile-gui.patch
Resolving www.ysbl.york.ac.uk... 144.32.72.243
Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3779 (3.7K) [text/plain]
Server file no newer than local file
`/home/hari/autobuild//sources/neil-jerram.guile-gui.patch' -- not
retrieving.

--2009-05-08 16:16:24--
http://www.ysbl.york.ac.uk/~emsley/software/extras/guile-gui-patch-post-neil.patch
Resolving www.ysbl.york.ac.uk... 144.32.72.243
Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 3799 (3.7K) [text/plain]
Server file no newer than local file
`/home/hari/autobuild//sources/guile-gui-patch-post-neil.patch' -- not
retrieving.

--2009-05-08 16:16:25--
http://download.gna.org/guile-lib/guile-lib-0.1.6.tar.gz
Resolving download.gna.org... 78.40.121.79
Connecting to download.gna.org|78.40.121.79|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 508682 (497K) [application/x-tar]
Server file no newer than local file
`/home/hari/autobuild//sources/guile-lib-0.1.6.tar.gz' -- not retrieving.

BUILDING coot: version coot-0.6-pre-1-revision-1994, python=yes
--2009-05-08 16:16:27--
http://www.ysbl.york.ac.uk/~emsley/software/pre-release/coot-0.6-pre-1-revision-1994.tar.gz
Resolving www.ysbl.york.ac.uk... 144.32.72.243
Connecting to www.ysbl.york.ac.uk|144.32.72.243|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 10851590 (10M) 

Re: [COOT] subversion build on ubuntu 9.04 fails : [: =: unary operator expected error

[Paul Emsley]

hari jayaram wrote:
Hi ..I tried a coot subversion (revision 1994) built-it-simple python on 
the newest ubuntu 9.04


The build crashes just after it builds guile and ( 16-coot.txt in the 
build directory ) reads :


checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... no
configure: error: guile required but not found
./build-it-gtk2-simple: line 2742: [: =: unary operator expected
NO need to update libtool 
/home/hari/autobuild/ex-charlie_2009-05-08__T20_14_49/coot-0.6-pre-1

make: *** No targets specified and no makefile found.  Stop.

This happens only on the new ubuntu (on a 32 bit 9.04 system) .
I was able to build this revision without any problem on Ubuntu 8.04 64 bit


Thanks update_libtool is not set sometimes, so using it as in 1994 is 
wrong.  I've tweaked the script.


But the problem for you lies above that..
 checking for guile... no
 configure: error: guile required but not found

Hmm!  what went wrong there..?

I'll try to build from scratch on Jaunty myself.

Cheers,

Paul.