Re: [COOT] coot-0.5-pre-1-906

[William G. Scott]

Yes, I've seen this appear essentially at random.  I don't have it on  
10.5.2 intel but do on 10.4.11 intel.  Moreover, 0.4.2 compiles ok but  
the newer one on that platform does not.  I have not been able to  
figure out what is going wrong.


There are some bugs in the iphone SDK -supplied compiler, but I don't  
think this is responsible for it.



On Apr 4, 2008, at 6:28 AM, Robert T Wyatt wrote:


Hi all (maintainer cc'd),

I'm staying home from work today so I finally have a little time to  
mention a couple of problems.


I'm on Mac OS 10.5.2 with the latest iPhone SDK (same error occurred  
prior to installing this) and an Intel MacBookPro.


With the latest coot, similar to the immediately preceding version,  
I get a bunch of these:


sed: 42: ./confstatKgEf4A/subs-3.sed: unescaped newline inside  
substitute pattern


... and then:

+/var/tmp/tmp.2.BPOqWx:22> touch c-interface-database.hh
+/var/tmp/tmp.2.BPOqWx:23> make coot_wrap_guile.cc
make: *** No rule to make target `coot_wrap_guile.cc'.  Stop.

Complete output is available here:
http://63.246.166.35/~robertwyatt/fink/coot-0.5-pre-1-906.txt


The immediately preceding version had similar problems:

config.status: creating auxil/vectors/Makefile
sed: file ./confstatqsItQP/subs-3.sed line 42: unterminated `s'  
command

config.status: executing depfiles commands
+/var/tmp/tmp.2.e3xTi9:20> /bin/rm -f src/coot_wrap_guile.cc src/ 
coot_wrap_guile_pre.cc src/coot_wrap_python.cc src/ 
coot_wrap_python_pre.cc

+/var/tmp/tmp.2.e3xTi9:21> cd src
+/var/tmp/tmp.2.e3xTi9:22> touch c-interface-database.hh
+/var/tmp/tmp.2.e3xTi9:23> make coot_wrap_guile.cc
make: *** No rule to make target `coot_wrap_guile.cc'.  Stop.

Complete output is available here:
http://63.246.166.35/~robertwyatt/fink/coot-0.5-pre-1-874.txt

I get these errors with and without fink's sed and/or ssed.

Happy to test potential solutions,
Robert

Re: [COOT] coot-0.5-pre-1-906

[William G. Scott]

Hi Robert:

I meant it seems random what platform/machine it appears on.  When it  
does, it is 100% reproducible.  So, for example, on my colleague's  
intel imac running 10.4.11, I get this error, but not on my intel  
imacs running 10.5.2.  I (like you) can't trace it to any other sed.   
Also I did say I do not think the new compiler is responsible for it,  
but was just noting that it also introduces problems (specifically,  
when compiling gfortran).


If you want to use the debian packages I compiled, they are here:

http://sage.ucsc.edu/fink_intel/10.5/unstable/main/binary-darwin-i386/sci/

Sorry for this.  I've reported the problem (including forwarding your  
email to the coot bb) and as soon as i figure out what to do I will  
fix it.


Bill



On Apr 4, 2008, at 6:57 AM, Robert T Wyatt wrote:

Just a comment: it's not random for me; it's consistent. Also, the  
same error occurred prior to installing the new SDK, so I also think  
it's unrelated. However, I'm not sure that another recent update  
(say to Apple's sed...?) isn't to blame.  --rtw


William G. Scott wrote:
Yes, I've seen this appear essentially at random.  I don't have it  
on 10.5.2 intel but do on 10.4.11 intel.  Moreover, 0.4.2 compiles  
ok but the newer one on that platform does not.  I have not been  
able to figure out what is going wrong.
There are some bugs in the iphone SDK -supplied compiler, but I  
don't think this is responsible for it.

On Apr 4, 2008, at 6:28 AM, Robert T Wyatt wrote:

Hi all (maintainer cc'd),

I'm staying home from work today so I finally have a little time  
to mention a couple of problems.


I'm on Mac OS 10.5.2 with the latest iPhone SDK (same error  
occurred prior to installing this) and an Intel MacBookPro.


With the latest coot, similar to the immediately preceding  
version, I get a bunch of these:


sed: 42: ./confstatKgEf4A/subs-3.sed: unescaped newline inside  
substitute pattern


... and then:

+/var/tmp/tmp.2.BPOqWx:22> touch c-interface-database.hh
+/var/tmp/tmp.2.BPOqWx:23> make coot_wrap_guile.cc
make: *** No rule to make target `coot_wrap_guile.cc'.  Stop.

Complete output is available here:
http://63.246.166.35/~robertwyatt/fink/coot-0.5-pre-1-906.txt


The immediately preceding version had similar problems:

config.status: creating auxil/vectors/Makefile
sed: file ./confstatqsItQP/subs-3.sed line 42: unterminated `s'  
command

config.status: executing depfiles commands
+/var/tmp/tmp.2.e3xTi9:20> /bin/rm -f src/coot_wrap_guile.cc src/ 
coot_wrap_guile_pre.cc src/coot_wrap_python.cc src/ 
coot_wrap_python_pre.cc

+/var/tmp/tmp.2.e3xTi9:21> cd src
+/var/tmp/tmp.2.e3xTi9:22> touch c-interface-database.hh
+/var/tmp/tmp.2.e3xTi9:23> make coot_wrap_guile.cc
make: *** No rule to make target `coot_wrap_guile.cc'.  Stop.

Complete output is available here:
http://63.246.166.35/~robertwyatt/fink/coot-0.5-pre-1-874.txt

I get these errors with and without fink's sed and/or ssed.

Happy to test potential solutions,
Robert

Re: [COOT] gtk2 version for redhat

[William G. Scott]

I made an rpm using alien from my ubuntu debian

Check the coot wiki

William G. Scott

(via iPod and gmail -- forgive the typos and brevity)

Please reply to [EMAIL PROTECTED]

On Apr 16, 2008, at 1:31 PM, hari jayaram <[EMAIL PROTECTED]> wrote:

Hi I noticed that there is no redhat gtk2 version of coot 0.5pre 1  
rev 958 or even earlier
I guess that means I am going to have to compile coot on my redhat  
machine to get access to the traffic-lights and other features


Can I cast my vote for a redhat python-gtk2 binary

Thanks
Hari

Re: [COOT] X-windows crashes while launching coot

[William G. Scott]

This sometimes happens if you are running compositing (like beryl,  
compwiz, etc) and have an older version of the graphics card driver  
software.


Turn off compositing (if indeed you are using it) and see if that works.

On Jun 26, 2008, at 12:13 PM, Jan Abendroth wrote:


Hi all,
after changing monitors from a CRT to a flat panel, and -most likely  
more
important- automatically updating the fedora packages, starting up  
coot

makes X-windows - last thing I saw was that coot read in the monomer
libraries.

On my black terminal it now says:
(gnome-panel:3933): GLib-GObject-CRITICAL **: g_object_run_dispose:
assertion ...

This only happens when I start coot on this computer. ssh to a  
different

machine and launching coot from there works, even though it runs very
sluggishly through the network.

Any ideas?

Thanks!
Jan

Re: [COOT] coot and fink (Mac OS X)

[William G. Scott]

Hi Andreas:

try


fink reinstall  gtkglext1   gtkglext1-shlib


and if you have $LD_LIBRARY_PATH and/or  $DYLD_LIBRARY_PATH set to  
anything, UNSET them (sorry, Paul).



Bill




On Jul 18, 2008, at 9:06 AM, Andreas Förster wrote:


Update on Bill Scott's email from yesterday.

On my system, 224 packages were marked for update or install (as  
dependencies).  With some tweaking, I got 170 or so to compile, but  
55 remained refractory because of circular dependencies.


I'm happy to report that these issues have mysteriously disappeared  
overnight.  Only coot and coot-shlibs fail to install with errors  
reproduced below.



Andreas


Bill, even after rerunning fink selfupdate and fink update-all, fink  
doesn't find GtkGLExt version 1.0.0.  Complete error:


checking for GtkGLExt - version >= 1.0.0... no
*** Could not run GtkGLExt test program, checking why...
*** The test program compiled, but did not run. This usually means
*** that the run-time linker is not finding GtkGLExt or finding the  
wrong
*** version of GtkGLExt. If it is not finding GtkGLExt, you'll need  
to set your
*** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to  
point
*** to the installed location  Also, make sure you have run ldconfig  
if that

*** is required on your system
***
*** If you have an old version installed, it is best to remove it,  
although
*** you may also be able to get things to work by modifying  
LD_LIBRARY_PATH

### execution of /var/tmp/tmp.2.ZJshe5 failed, exit code 1
Failed: phase compiling: coot-0.5-pre-1-1223-1 failed


(dyn1216-120) ~: fink list GtkGLExt
Information about 6991 packages read in 1 seconds.
i   gtkglext1  1.0.6-1007OpenGL Extension to GTK
i   gtkglext1-shlibs   1.0.6-1007OpenGL Extension to GTK
gtkglextmm 1.2.0-1003C++ wrapper for GtkGLExt
gtkglextmm-shlibs  1.2.0-1003C++ wrapper for GtkGLExt


William Scott wrote:

Hi folks:
If you use fink to install coot on Mac OS X, you will find a lot of  
stuff needs to be updated.  This is because fink has done a large- 
scale update based on the new gnome/gtk+2 pango/cairo libraries, so  
don't be alarmed if you are asked to update 100s of packages  
simultaneously.
To ease the burden, I am putting precompiled versions of everything  
on our servers for 10.4/10.5 ppc/intel and 10.5 intel.  The intel  
ones are available now and the ppc one should be ready in the next  
few hours.

cf  http://tinyurl.com/fink-precompiled
for more info. on how to do this.
Bill
PS:  On one machine, I was forced to issue
fink rebuild pango1-xft2-shlibs; fink reinstall pango1-xft2-shlibs  
pango1-xft2
fink rebuild pango1-xft2-ft219 ; fink reinstall pango1-xft2-ft219  
pango1-xft2-ft219-shlibs pango1-xft2-ft219-dev

to correct a conflict.

Re: [COOT] A small question

[William G. Scott]

On Jul 18, 2008, at 10:23 AM, David Margulies wrote:

I removed the tips-gui.scm file from the scheme directory, and now  
coot
launches fine.  I’m not quite sure what that means, perhaps the tips- 
gui.scm


That is interesting.  The tips annoy me so I have it turned off by  
default, and when I went to try to reproduce your problem, I couldn't  
get it to come on again (removing .coot and so forth).

Re: [COOT] coot and fink (Mac OS X)

[William G. Scott]

I had not set $LD_LIBRARY_PATH.  Changing it to /sw/lib and back  
didn't make a difference.  $DYLD_LIBRARY_PATH is set to /Users/ 
andreas/Computer/ImageMagick-6.4.1/lib:/usr/local/ccp4-6.0.2/lib

That's not expected to interfere with fink, is it?


Setting DYLD_LIBRARY_PATH is usually poison.

Anyway, I just committed coot 0.5-pre-1-1278  to fink cvs.  In its  
build script, I explicitly now issue


DYLD_LIBRARY_PATH=""

before configure (which works on my machines at least).

Could you please try that one and see if it works?

Thanks.

Bill

Re: [COOT] A small question

[William G. Scott]

OK, I found the problem:

% grep "#\!" scheme/*.scm
scheme/coot-gui.scm:#!/home/paule/build/bin/guile -s
scheme/tips-gui.scm:#!/home/paule/build/bin/guile -s

This can be fixed by removing those lines from the two scheme files.

In addition, the last two lines of the tips-gui.scm file need to be  
uncommented in order to actually get the annoying tips pop-up to appear.


I have no idea why it failed silently for me but created problems for  
others (and there was at least one other that I now think was the same  
problem).



On Jul 18, 2008, at 10:37 AM, William G. Scott wrote:



On Jul 18, 2008, at 10:23 AM, David Margulies wrote:

I removed the tips-gui.scm file from the scheme directory, and now  
coot
launches fine.  I’m not quite sure what that means, perhaps the  
tips-gui.scm


That is interesting.  The tips annoy me so I have it turned off by  
default, and when I went to try to reproduce your problem, I  
couldn't get it to come on again (removing .coot and so forth).

Re: [COOT] ipod version of coot?

[William G. Scott]

I bought the $10 software upgrade for my wife's iPod (they sell you  
the software that permits you to buy yet more stuff) and this was the  
only app we downloaded so far.  It doesn't connect the bonds on RNA or  
at least gp120.  Just a pile of atoms. So there is still a need for an  
iCoot...



On Jul 28, 2008, at 10:17 AM, Donnie Berkholz wrote:


On 10:01 Mon 28 Jul , William G. Scott wrote:

This is via VNSea (jailbroken ipod), but it got me thinkin'...


There's already a neat, new, about-to-be-BSD-licensed app called
Molecules for viewing, which is about all you could do on an
iPhone/iPod. Here's a blog post describing it:

http://www.sunsetlakesoftware.com/2008/07/10/molecules-iphone-and-ipod-touch

--
Thanks,
Donnie

Donnie Berkholz
Developer, Gentoo Linux
Blog: http://dberkholz.wordpress.com

Re: [COOT] coot fink upgrade and gtk+2 issues

[William G. Scott]

Hi Jan:

This is a bug in gtk+2 package.

Issue

fink remove gtk+2-dev

and try the

sudo apt-get install gtk+2

and hopefully that will make it right.

Bill


William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/


On Aug 1, 2008, at 8:36 AM, Jan Abendroth wrote:


Hi all,
I did a rather unfortunate "update" of coot using
"apt-get update, apt-get install coot"
At some point I get messages such as:
"Preparing to replace gtk+2 2.12.10-1...
...
### excecution of /sw/bin/dpkg-lockwait failed, exit code 1
Failed: can't install package gtk+2-2.12.10-1"
Similar things happen with fink (fink selfupdate, fink install coot)

... the update also removed my previous running version... only got to
install the self-contained vsn 0.4.1 from Bill's page, which  
unfortunately
does not have some of my currently favourite features such as the  
very nice

ncs commands.

Any ideas? ... btw. osx 10.4

Thanks!
Jan

Re: [COOT] crash when trying to run refmac

[William G. Scott]

Hi Paul:

I'm getting this too.   If I open an mtz file without phases, refmac  
runs a refinement and makes a map.


If I then try to invoke refmac, coot crashes (in my case without error  
messages).


% coot --version
0.5-pre-1 (revision 1282)  [with guile 1.8.3 embedded] [with python  
2.5.2 embedded]


Bill


On Aug 3, 2008, at 2:04 PM, Paul Emsley wrote:


Paul Paukstelis wrote:
When I try to run a refmac job from coot everything crashes with a  
bunch of

these:
warning: .dynamic section for "/usr/lib/libgdk_pixbuf-2.0.so.0" is  
not at

the expected address
system: fedora 8 x86_64
version: 0.5-pre
Library issue?


Yes, I guess so.


Any thoughts?


I think that this is caused by running  a 32 bit binary on a 64 bit  
OS (but maybe there was some interesting other errrors thatgot  
snipped). I don't know what to advise.  I guess that there are  
others on this list who have more experience with 32 vs 64 bit than I.


I think that'd I better get on and start making 64 bit binaries.  Hmm.

> Other than that, everything seems to work fine.

Well, that's good to know.

Paul.

Re: [COOT] coot fink upgrade and gtk+2 issues

[William G. Scott]

Hi Jan:

I am glad it is working now.  It really shouldn't have been that  
problematic, and I apologize. Unfortunately, I have no idea why these  
things wouldn't work the first time around.


Bill



On Aug 5, 2008, at 9:31 AM, Jan Abendroth wrote:


Thanks, Bill,
that was a great hint! Even though sudo apt-get intall gtk+2 did not  
work, I
poked around a bit more. Eventually fink reinstalling the four  
packages you
mentioned earlier individually and the fink reinstall coot did the  
trick

:-))
Now everything works again.
Thanks a lot for your help!
Jan

2008/8/4 William G. Scott <[EMAIL PROTECTED]>


what happens if you just try

sudo apt-get install gtk+2

again?

It installed the shlibs ok, so I am really not sure.  Sometimes you  
just

have to coax it along...  Well, you shouldn't HAVE to, but ours is an
imperfect world...


On Aug 4, 2008, at 10:29 PM, Jan Abendroth wrote:

thanks, Bill,

yet: n - sounded so got, yet it did not do the trick either, see
below. Seems like something is mighty confused...
is there something in fink to force installation etc or to purge  
what it

thinks it has installed?

Cheers
Jan


The following 4 packages will be reinstalled:
gtk+2 gtk+2-shlibs libpng3 libpng3-shlibs
Reading buildlock packages...
/sw/bin/dpkg-lockwait -i
/sw/var/cache/apt/archives/gtk+2_2.12.10-1_darwin-i386.
deb /sw/var/cache/apt/archives/gtk+2-shlibs_2.12.10-1_darwin- 
i386.deb
(Reading database ... 43372 files and directories currently  
installed.)

Preparing to replace gtk+2 2.12.10-1 (using
.../gtk+2_2.12.10-1_darwin-i386.deb)
...
Unpacking replacement gtk+2 ...
Preparing to replace gtk+2-shlibs 2.12.10-1 (using
.../gtk+2-shlibs_2.12.10-1_da
rwin-i386.deb) ...
Unpacking replacement gtk+2-shlibs ...
Setting up gtk+2-shlibs (2.12.10-1) ...
Setting up gtk+2 (2.12.10-1) ...
### execution of /sw/bin/dpkg-lockwait failed, exit code 1
Failed: can't batch-install packages:
/sw/var/cache/apt/archives/gtk+2_2.12.10-1
_darwin-i386.deb
/sw/var/cache/apt/archives/gtk+2-shlibs_2.12.10-1_darwin-i386.d
eb



On Aug 3, 2008, at 11:37 PM, William G. Scott wrote:

Well, it is guessing time, but hopefully this might unstick stuff:


try:

fink reinstall libpng3-shlibs  libpng3  gtk+2  gtk+2-shlibs


I'm guessing based on the first few lines of the appended output,  
so I
apologize in advance if this doesn't help.  It might also help to  
start a
new shell session after the fink reinstall, just in case the  
environment
variables need to be initialized.  It sounds like there are 10  
packages

trapped in debian purgatory.

On Aug 3, 2008, at 11:24 PM, Jan Abendroth wrote:

thanks for your reply, Bill.

However, things still don't work our:

bash: fink remove gtk+2-dev
Information about 3990 packages read in 3 seconds.
WARNING: gtk+2-dev is not installed, skipping.
Nothing removed
same for gtk+2, gtk, ...

bash: sudo apt-get install gtk+2
gives a lengthy message and dies, see end of email

Any ideas?
Thanks!
Jan

message from apt-get install gtk+2:
Reading Package Lists... Done
Building Dependency Tree... Done
Sorry, gtk+2 is already the newest version.
0 packages upgraded, 0 newly installed, 0 to remove and 2  not  
upgraded.

10 packages not fully installed or removed.
Need to get 0B of archives. After unpacking 0B will be used.
Setting up gtk+2 (2.12.10-1) ...
g_module_open() failed for /sw/lib/gtk-2.0/2.10.0/loaders/io- 
wmf.so:

dlopen(/sw/
lib/gtk-2.0/2.10.0/loaders/io-wmf.so, 10): Library not loaded:
/sw/lib/libpng12.
0.dylib
Referenced from: /sw/lib/libwmf-0.2.7.dylib
Reason: Incompatible library version: libwmf-0.2.7.dylib requires
version 30.0
.0 or later, but libpng12.0.dylib provides version 19.0.0
g_module_open() failed for
/sw/lib/gtk-2.0/2.10.0/loaders/libpixbufloader-png.so
: dlopen(/sw/lib/gtk-2.0/2.10.0/loaders/libpixbufloader-png.so,  
10):

Library not
loaded: /sw/lib/libpng12.0.dylib
Referenced from: /sw/lib/gtk-2.0/2.10.0/loaders/libpixbufloader- 
png.so
Reason: Incompatible library version: libpixbufloader-png.so  
requires

version
30.0.0 or later, but libpng12.0.dylib provides version 19.0.0
dyld: Library not loaded: /sw/lib/libpng12.0.dylib
Referenced from: /sw/bin/gtk-query-immodules-2.0
Reason: Incompatible library version: gtk-query-immodules-2.0  
requires

version
30.0.0 or later, but libpng12.0.dylib provides version 19.0.0
/sw/sbin/update-gtk-immodules: line 15:  1355 Trace/BPT trap
gtk-query-
immodules-2.0 >$TMPFILE
/sw/bin/dpkg: error processing gtk+2 (--configure):
subprocess post-installation script returned error exit status 133
dpkg: dependency problems prevent configuration of gtk2-engines:
gtk2-engines depends on gtk+2 (>= 2.12.0-1); however:
Package gtk+2 is not configured yet.
/sw/bin/dpkg: error processing gtk2-engines (--configure):
dependency problems - leaving unconfigured
dpkg: dependency problems prevent configuration of
gnome-themes-glossy-p:
gnome-themes-glossy-p depends on gtk+2 (>= 2.12.0-1); however:

Re: [COOT] fonts in coot 0.5 pre1

[William G. Scott]

You can make a file called
~/.gtkrc-2.0

and put in it

gtk-font-name = "Sans 10"

(or whatever font size suits you).

and for an OS-X native look,

include "/sw/share/themes/Glossy_P/gtk-2.0/gtkrc"


You can also create a system-wide version of the file

/sw/etc/gtk-2.0/gtkrc

and put those lines in there.

Check also to make sure you don't have the line

gtk-font-name = "LucidaGrande 15"

it is obsolete with the new pango-cairo coot.




On Aug 8, 2008, at 7:34 AM, Joe Jaeger wrote:


Hi Bill

Ive been running coot on my Intel Laptop (Processor Name:	Intel Core  
2 Duo Processor Speed:	2.4 GHz  Number Of Processors 1  Total Number  
Of Cores:	2) these days. Your build is fully functional and stable  
it seems, but the the gui-fonts are kinda big for the laptop  
screen.  Is there any way to tweak this and make them smaller.  I've  
not been able to find the right settings/ files etc.  Is the font  
size determined  at time of compilation??


--JJ


Joachim Jaeger DPhil
Wadsworth Center NYS DOH
Assoc. Prof. SUNY Albany
150 New Scotland Ave
Albany NY 12208

Re: [COOT] Installing Coot on a Mac 10.5.4

[William G. Scott]

Try this:

1.  Be sure "unstable" is activated in /sw/etc/fink.conf

2.  fink selfupdate
3.  fink update-all

If it is still whining, try

fink  rebuild  foo ; fink reinstall foo

for any package foo that seems problematic.

I have no idea why, but this has helped others in the past.  I don't  
understand the origin of the problem.


Bill


William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/


On Aug 17, 2008, at 2:33 PM, Ricardo Leal wrote:


Dear all,

I have been trying to install Coot through Fink. I have been  
following the instructions on

William Scott's OS X Scientific Computing webpage:
% sudo apt-get install coot

Sorry, but the following packages have unmet dependencies:
 coot: Depends: librsvg2-shlibs (>= 2.20.0-1) but 2.9.5-11 is to be  
installed
   Depends: librsvg2-gtk (>= 2.20.0-1) but 2.9.5-11 is to be  
installed

E: Sorry, broken packages

I've noticed the packages I have do not correspond to the versions  
needed:


fink list librsvg*
Scanning package description files..
Information about 2531 packages read in 0 seconds.
i   librsvg2 2.9.5-11 SAX-based render library for SVG  
files
librsvg2-bin 2.9.5-11 SAX-based render library for SVG  
files

i   librsvg2-gtk 2.9.5-11 Enable GTK to use SVG data
i   librsvg2-shlibs  2.9.5-11 SAX-based render library for SVG  
files


I have configured fink to install unstable packages and apparently  
it indexes the unstable

sources:
% fink selfupdate; fink index; fink scanpackages
(...)
Hit http://sage.ucsc.edu unstable/crypto Packages
Hit http://sage.ucsc.edu unstable/crypto Release
(...)
However, when I try to reinstall the librsvg2 I still get the same  
version...


% fink --trees=unstable reinstall librsvg2
Scanning package description files
Information about 254 packages read in 0 seconds.
Failed: no package found for specification 'librsvg2'!
%  fink reinstall librsvg2
Scanning package description files..
Information about 2531 packages read in 1 seconds.
The following package will be reinstalled:
librsvg2
Reading buildlock packages...
/sw/bin/dpkg-lockwait -i /sw/var/cache/apt/archives/ 
librsvg2_2.9.5-11_darwin-i386.deb
(Lecture de la base de données... 22098 fichiers et répertoires déjà  
installés.)
Préparation du remplacement de librsvg2 2.9.5-11 (en utilisant .../ 
librsvg2_2.9.5-

11_darwin-i386.deb) ...
Dépaquetage de la mise à jour de librsvg2 ...
Paramétrage de librsvg2 (2.9.5-11) ...

Any help you can give me will be very much appreciated!
Thanks in advance,
Ricardo

Re: [COOT] Installing Coot on a Mac 10.5.4

[William G. Scott]

Dear Francis et al:

I just encountered the same problem setting up a laptop.

There were a couple of things causing this problem:

1.  After using the binary installer, I had to change it to use the  
unstable branch of fink, and then use


fink selfupdate-cvs

to change it from point release updates to continuously available ones.

2.  To get it to build anything missing or overlooked from my binary  
distribution, but to use everything available,


fink -b install coot


I hope this is of use to someone in the future.

Sorry for this being problematic.


Bill




On Aug 17, 2008, at 8:54 PM, Francis E Reyes wrote:


Bill

When I had to deal with this, I think it was the problematic package  
was gnome-vfs2-unified-shlibs.


You are providing librsvg2 2.20.0-1 . The problem is that that this  
requires gnome-vfs2-unified-shlibs (>= 1:2.20.0-1) . The latest  
binary distribution on fink is 2.9.5-11. You don't provide gnome- 
vfs2-unified-shlibs on sage.ucsc.edu/fink_ppc/unstable/main/binary- 
darwin-powerpc/gnome/ so fink reverts to the binary distribution on  
their main servers which doesn't fulfill the requirement.   
Interestingly, apt-get install librsvg2-shlibs complains about gnome- 
vfs2-unified-shlibs. ( At least if I recall correctly when I had  
this problem )


The solution might be to provide gnome-vfs2-unified-shlibs @  
2.20.0-1 (including its dependencies) on sage.ucsc.edu.




Maybe this helps?

Cheers
FR
P.s. thanks for providing the binary distributions btw. Saves me a  
lot of compile time and disk space our lab doesn't have :)



On Aug 17, 2008, at 7:09 PM, William G. Scott wrote:


Try this:

1.  Be sure "unstable" is activated in /sw/etc/fink.conf

2.  fink selfupdate
3.  fink update-all

If it is still whining, try

fink  rebuild  foo ; fink reinstall foo

for any package foo that seems problematic.

I have no idea why, but this has helped others in the past.  I  
don't understand the origin of the problem.


Bill


William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/


On Aug 17, 2008, at 2:33 PM, Ricardo Leal wrote:


Dear all,

I have been trying to install Coot through Fink. I have been  
following the instructions on

William Scott's OS X Scientific Computing webpage:
% sudo apt-get install coot

Sorry, but the following packages have unmet dependencies:
coot: Depends: librsvg2-shlibs (>= 2.20.0-1) but 2.9.5-11 is to be  
installed
 Depends: librsvg2-gtk (>= 2.20.0-1) but 2.9.5-11 is to be  
installed

E: Sorry, broken packages

I've noticed the packages I have do not correspond to the versions  
needed:


fink list librsvg*
Scanning package description files..
Information about 2531 packages read in 0 seconds.
i   librsvg2 2.9.5-11 SAX-based render library for SVG  
files
  librsvg2-bin 2.9.5-11 SAX-based render library for SVG  
files

i   librsvg2-gtk 2.9.5-11 Enable GTK to use SVG data
i   librsvg2-shlibs  2.9.5-11 SAX-based render library for SVG  
files


I have configured fink to install unstable packages and apparently  
it indexes the unstable

sources:
% fink selfupdate; fink index; fink scanpackages
(...)
Hit http://sage.ucsc.edu unstable/crypto Packages
Hit http://sage.ucsc.edu unstable/crypto Release
(...)
However, when I try to reinstall the librsvg2 I still get the same  
version...


% fink --trees=unstable reinstall librsvg2
Scanning package description files
Information about 254 packages read in 0 seconds.
Failed: no package found for specification 'librsvg2'!
%  fink reinstall librsvg2
Scanning package description files..
Information about 2531 packages read in 1 seconds.
The following package will be reinstalled:
librsvg2
Reading buildlock packages...
/sw/bin/dpkg-lockwait -i /sw/var/cache/apt/archives/ 
librsvg2_2.9.5-11_darwin-i386.deb
(Lecture de la base de données... 22098 fichiers et répertoires  
déjà installés.)
Préparation du remplacement de librsvg2 2.9.5-11 (en utilisant .../ 
librsvg2_2.9.5-

11_darwin-i386.deb) ...
Dépaquetage de la mise à jour de librsvg2 ...
Paramétrage de librsvg2 (2.9.5-11) ...

Any help you can give me will be very much appreciated!
Thanks in advance,
Ricardo

[COOT] can coot link to fftw3?

[William G. Scott]

If so, how do you tell configure?

Thanks.


William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/

Re: [COOT] can coot link to fftw3?

[William G. Scott]

Hi Kevin:

My problem is this:

If coot (the binary itself) links to fftw v. 2.1.5, it crashes,  
reporting a memory conflict error, upon trying to calculate a map.   
(This happens whether I link to dynamic or static libraries, contrary  
to my previous report to Paul.)  If coot links to fftw v. 2.0.7,  
supplied by ccp4, it works properly.


Any ideas?

Bill

William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/


On Sep 2, 2008, at 6:58 AM, Kevin Cowtan wrote:


No, it can't. Clipper only speaks to fftw v2.

If fftw v2 is a problem, you can build clipper without fftw at all  
by using the kiss-fft overlay which removes the fftw dependence.

http://www.ysbl.york.ac.uk/~cowtan/clipper/loveboat.html
That saves one dependency, but the calculation of maps will become  
2-3x slower.


However I don't think the autoconf knows about this, so it'll need  
some hacking.


William G. Scott wrote:

If so, how do you tell configure?
Thanks.
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/

Re: [COOT] can coot link to fftw3?

[William G. Scott]

Thanks Tim and everyone for suggestions.

I finally got it to work by linking the single-precision libraries:

zsh-% otool -L /sw/bin/coot | grep fft
/sw/lib/libsrfftw.2.dylib (compatibility version 3.0.0,  
current version 3.7.0)
/sw/lib/libsfftw.2.dylib (compatibility version 3.0.0,  
current version 3.7.0)





On Sep 2, 2008, at 10:20 AM, Tim Fenn wrote:


On Tue, 2 Sep 2008 07:27:17 -0700 "William G. Scott"
<[EMAIL PROTECTED]> wrote:


Hi Kevin:

My problem is this:

If coot (the binary itself) links to fftw v. 2.1.5, it crashes,
reporting a memory conflict error, upon trying to calculate a map.
(This happens whether I link to dynamic or static libraries,
contrary to my previous report to Paul.)  If coot links to fftw v.
2.0.7, supplied by ccp4, it works properly.



try compiling clipper with -fno-strict-aliasing, or drop the
optimization flags to -O1 or lower.

HTH,
Tim

--
-

   Tim Fenn
   [EMAIL PROTECTED]
   Stanford University, School of Medicine
   James H. Clark Center
   318 Campus Drive, Room E300
   Stanford, CA  94305-5432
   Phone:  (650) 736-1714
   FAX:  (650) 736-1961

-

Re: [COOT] fftw-shlibs vs fftw-mpi-shlibs (OS X)

[William G. Scott]

Dear Andreas et al:

My post to the cootbb on this never made it.

I've fixed the coot package to use gpp4, mmdb, ssm, clipper, and  
fftw(2) rather than ccp4-onlylibs-dev, which will cut down on the  
installation overhead in the future (these packages are minimal).   
fftw(3) is not compatible with fftw(2).  fftw(2) is "legacy" but  
almost everyone in crystallography still seems to use it.


fftw-mpi is a variant of fftw and a superset.  It allows the  
calculation to be split among multiple processors.  For coot it  
doesn't matter, but if you already had fftw-mpi installed, coot  
shouldn't force installation of the other one (since it is a subset  
anyway).  Previously I had coot link to static fftw built in ccp4- 
onlylibs-dev.


I've also updated the ccp4 package to fix (I hope) compilation and run- 
time problems.  It built fine for me on 4 different machines.


I've put more details here:

http://tinyurl.com/cootccp4changes

I've also fixed a couple of shlibs packaging errors. As a consequence,  
you will probably have to issue the command


fink install coot

TWICE.  The second time it goes really quickly (it only unpacks the  
debian file).


Similarly for ccp4.

As always, you can grab my debian packages and avoid the overhead of  
compiling:

http://tinyurl.com/fink-precompiled

All the best,

Bill




On Sep 12, 2008, at 2:52 AM, Andreas Förster wrote:


Hey there,

running fink update-all, I'm asked for help in picking a package to  
satisfy a virtual dependency, with fftw-shlibs and fftw-mpi-shlibs  
presented as alternatives.  Coot as well as ccp4 have in their list  
of dependencies fftw-shlibs | fftw-mpi-shlibs, indicating that I can  
go with either.  But what's the difference?  Why are there two  
packages? They're both maintained by the Sebastien Maret, are at the  
same version and perform the same task (DFT in one or more  
dimensions, of both real and complex data, for arbitrary input size).


Currently on my Leppard system, I have fftw3 and fftw3-shlibs  
installed (I didn't follow Kevin's recent posts on the subject), but  
not any fftw-related package in version 2.  Coot has always compiled  
fine, whereas ccp4 never has.


Thanks.


Andreas




--
   Andreas Förster, Research Associate
   Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London

[COOT] coot 0.5-pre-1-1391 stand-alone for intel OS X (10.5.4).

[William G. Scott]

Hi folks:

I've put a self-contained intel 10.5.4 coot here:  
http://tinyurl.com/coot-on-osx
so stop with the death threats.

If you use this, please make sure you have the latest X11.app from
http://trac.macosforge.org/projects/xquartz

I no longer have access to OS X 10.4.

I'll try to make one for ppc in the next day or two.

As mentioned, I have streamlined the fink version, so if you want to  
keep up to date, that
is always a better option.  (I've used fink to make the stand-alone,  
so you aren't being any

more pure by using this.)

Peace and joy,

Bill

Re: [COOT] coot 0.5-pre-1-1391 stand-alone for intel OS X (10.5.4).

[William G. Scott]

Thanks.  The ppc one is now on the same page.

Now I need to go find out who my kids now are calling "daddy" in my  
absence.



On Sep 12, 2008, at 7:35 PM, Juergen Bosch wrote:


Works as advertised, I guess you deserve your weekend now :-)

Thanks,

Jürgen

P.S. fancy new X11 icon

On 12 Sep 2008, at 18:54, William G. Scott wrote:


Hi folks:

I've put a self-contained intel 10.5.4 coot here:  
http://tinyurl.com/coot-on-osx
so stop with the death threats.

If you use this, please make sure you have the latest X11.app from
http://trac.macosforge.org/projects/xquartz

I no longer have access to OS X 10.4.

I'll try to make one for ppc in the next day or two.

As mentioned, I have streamlined the fink version, so if you want  
to keep up to date, that
is always a better option.  (I've used fink to make the stand- 
alone, so you aren't being any

more pure by using this.)

Peace and joy,

Bill


-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone:   +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch

[COOT] OS X 10.5.5 update and X11

[William G. Scott]

Hi folks:

My apologies to those who will find this irrelevant, but hopefully  
they didn't read beyond the subject line.  I've gotten many questions  
about this, so ...


After the update to 10.5.5, you have to update (again) X11, preferably  
to 2.3.1.


Why Apple didn't include this in the 10.5.5 is anyone's guess, but  
there is an official update available here:


http://xquartz.macosforge.org/trac/wiki

This is the real thing, made by the real Apple X11 developer.

I installed it and everything is working as well as ever.

Except stereo in X11, but we can keep hoping...


Bill Scott

Re: [COOT] Coot 0.5 released

[William G. Scott]

Hi Mark:

My 10.4 G4 is lying in a heap of smoldering rubble at work on what  
would be my dining room table if I was paid enough to own a real  
house, along with heaps of wreckage that represent various stages in  
the life cycle of the SGI (including some from Alice). (The SGIs, to  
their credit, still work, even if there hasn't been an OS update in 10  
years.)


I did a security update on my trusty G4, xanana (named for the East  
Timor Fretilin rebel leader and subsequent president) and it would not  
reboot.  Apple said it needed a new processor board, which would cost  
more than an iMac that is about 10X faster.


So, it is gone the way of the SGI.

I'm right now making bundles for 10.5 intel and ppc.

If anyone has a 10.4 ppc machine and is willing to do this, I will be  
happy to tell you how. (Basically I just configure a new fink  
installation to build in /usr/local/xtal/coot and then weed out as  
much as possible).


Sorry.  At least it lasted longer than an iPod.

Bill



On Sep 24, 2008, at 7:44 AM, Mark Collins wrote:


you're all quackers :-)

Will somebody be putting a mac G4 10.4 bundle together, for the new
version? Please, pretty please!

Mark

Re: [COOT] Coot 0.5 released

[William G. Scott]

Hi David:

I've got 10.5 covered, and 10.4 ppc (thanks to Luca Jovine!) is on its  
way.


If you would help with 10.4 intel, that would be fantastic.

Bill


On Sep 24, 2008, at 10:51 AM, David Briggs wrote:


OSX 10.4 Intel???

If that's not being done elsewhere, I can volunteer to give it a go...

Cheers,

Dave

2008/9/24 Tim Kirk <[EMAIL PROTECTED]>:

We got one here at YSBL.

Let me know what to do and I'll set it doing it.

Given it came from Paul & Kevin's grant from memory it seems only  
fair to

use it this way!

Cheers,

Tim


On 24 Sep 2008, at 16:08, William G. Scott wrote:


Hi Mark:

My 10.4 G4 is lying in a heap of smoldering rubble at work on what  
would
be my dining room table if I was paid enough to own a real house,  
along with
heaps of wreckage that represent various stages in the life cycle  
of the SGI
(including some from Alice). (The SGIs, to their credit, still  
work, even if

there hasn't been an OS update in 10 years.)

I did a security update on my trusty G4, xanana (named for the  
East Timor
Fretilin rebel leader and subsequent president) and it would not  
reboot.
Apple said it needed a new processor board, which would cost more  
than an

iMac that is about 10X faster.

So, it is gone the way of the SGI.

I'm right now making bundles for 10.5 intel and ppc.

If anyone has a 10.4 ppc machine and is willing to do this, I will  
be
happy to tell you how. (Basically I just configure a new fink  
installation
to build in /usr/local/xtal/coot and then weed out as much as  
possible).


Sorry.  At least it lasted longer than an iPod.

Bill



On Sep 24, 2008, at 7:44 AM, Mark Collins wrote:


you're all quackers :-)

Will somebody be putting a mac G4 10.4 bundle together, for the new
version? Please, pretty please!

Mark








--

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile

Re: [COOT] Coot 0.5 released

[William G. Scott]

Hi David:

Here is how I am doing it.  I hope you don't mind that I am cc-ing this.

I picked a directory that I hope will be uninhabited:

/usr/local/xtal/coot

1.  sudo mkdir -p /usr/local/xtal

2.  Download fink's source code and compile it, using /usr/local/xtal/ 
coot as the prefix. You'll need the latest Xcode (3.1 I think) and X11  
(2.3.1).  Use the bootstrap install, and it will prompt you to specify  
the directory.  /sw is the default, but you can tell it to use  /usr/ 
local/xtal/coot


3.  Run the bootstrap.  When prompted, tell it to use unstable  
packages.  When done,


source  /usr/local/xtal/coot/bin/init.sh

fink selfupdate-rsync

fink install coot

You can hack the fftw.info file and remove all references to fortran  
extensions, and that will save about 3 hours of compiling gcc3.4,  
which gives you gfortran, which, as far as I can tell, is useless in  
this context.


I then move   /usr/local/xtal/coot/bin/coot to  /usr/local/xtal/coot/ 
bin/coot.ppc  and then write a wrapper shell script with the line

 source /usr/local/xtal/coot/bin/init.sh
before invocation of the actual coot binary.  This ensures the user  
will have the proper run-time environment but not contaminate the rest  
of his or her setup.  I also modify  /usr/local/xtal/coot/etc/gtk-2.0/ 
gtkrc  to use the aqua -like buttons for the interface.  The  
description of this is in the coot.info file.


4.  Then when it is done, I test it and verify it is working, and then  
tar everything up for next time, and then remove all the spurious  
files and directories, so that the download will be "only" about 120 MB.



Bill




On Sep 24, 2008, at 1:56 PM, David Briggs wrote:


Hi Bill,

happy to help out...

If you can give me a quick bullet point guide to
"not-making-a-mess-of-compiling-coot", then that'd be great.
(What compiler to use, etc.)

A bit new to this, but eager to learn.

Cheers,

Dave

2008/9/24 William G. Scott <[EMAIL PROTECTED]>:

Hi David:

I've got 10.5 covered, and 10.4 ppc (thanks to Luca Jovine!) is on  
its way.


If you would help with 10.4 intel, that would be fantastic.

Bill


On Sep 24, 2008, at 10:51 AM, David Briggs wrote:


OSX 10.4 Intel???

If that's not being done elsewhere, I can volunteer to give it a  
go...


Cheers,

Dave

2008/9/24 Tim Kirk <[EMAIL PROTECTED]>:


We got one here at YSBL.

Let me know what to do and I'll set it doing it.

Given it came from Paul & Kevin's grant from memory it seems only  
fair to

use it this way!

Cheers,

Tim


On 24 Sep 2008, at 16:08, William G. Scott wrote:


Hi Mark:

My 10.4 G4 is lying in a heap of smoldering rubble at work on  
what would
be my dining room table if I was paid enough to own a real  
house, along

with
heaps of wreckage that represent various stages in the life  
cycle of the

SGI
(including some from Alice). (The SGIs, to their credit, still  
work,

even if
there hasn't been an OS update in 10 years.)

I did a security update on my trusty G4, xanana (named for the  
East

Timor
Fretilin rebel leader and subsequent president) and it would not  
reboot.
Apple said it needed a new processor board, which would cost  
more than

an
iMac that is about 10X faster.

So, it is gone the way of the SGI.

I'm right now making bundles for 10.5 intel and ppc.

If anyone has a 10.4 ppc machine and is willing to do this, I  
will be

happy to tell you how. (Basically I just configure a new fink
installation
to build in /usr/local/xtal/coot and then weed out as much as  
possible).


Sorry.  At least it lasted longer than an iPod.

Bill



On Sep 24, 2008, at 7:44 AM, Mark Collins wrote:


you're all quackers :-)

Will somebody be putting a mac G4 10.4 bundle together, for the  
new

version? Please, pretty please!

Mark








--

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile








--

David C. Briggs PhD
Father & Crystallographer
http://drdavidcbriggs.googlepages.com/home
AIM ID: dbassophile

Re: [COOT] Coot 0.5 released

[William G. Scott]

Yes, I put coot 0.5.0 into fink cvs, both "stable" and "unstable"  
yesterday. Barring bug fixes, I won't touch the stable entry until 0.6  
is released.


fink selfupdate-rsync

or

fink selfupdate-cvs

I've also built these on my 10.5 machines so they are available as  
fink binary debian packages.




On Sep 24, 2008, at 9:21 PM, Felix Frolow wrote:


Dear Bill it was fast
BTW is it possible to install new coot also via FINK?

Re: [COOT] mac 10.4 coot 5 error?

[William G. Scott]

If you have a .gtkrc-2.0  file specifying a font, comment that line out.



On Oct 2, 2008, at 12:09 PM, Mark Collins wrote:


Hi
I want to know if the following error will affect the running of  
coot?  It seems to start up fine except for this error.

Thanks Mark


I get the following error in my start up log:

PDB file /usr/local/xtal/coot/share/coot/standard-residues.pdb has  
been read.

Spacegroup: P 1 Cell: 40.631 109.18 93.243 90 90 90
(coot.ppc:457): Pango-WARNING **: Error loading GDEF table 28333
(coot.ppc:457): Pango-WARNING **: Error loading GSUB table 28333
(coot.ppc:457): Pango-WARNING **: Error loading GPOS table 28333
initalize graphics molecules...done.
(filter-fileselection-filenames-state)


I installed fink in /usr/local/xtal/ as described by Bill Scott  
here.  I then download and unpacked the standalone coot tarball  
generously provided by Bill (I previously had this issue with just  
the coot tarball).

I then issued;
fink rebuild gmp
fink reinstall gmp gmp-shlibs
to get around the libgmp problem

But I get this weird pango error (above).

Other thing to note is that the /usr/local/xtal/coot/etc/gtk-2.0/ 
gtkrc file is currently contains;


include "/usr/local/xtal/coot/share/themes/Glossy_P/gtk-2.0/gtkrc"
gtk-font-name = "Sans 11"

Re: [COOT] Atoms

[William G. Scott]

All un-fsck options should be non-default optional, lest they create  
other problems.


On Oct 2, 2008, at 6:27 PM, Charlie Bond wrote:

How straightforward would it be to modify coot to automatically 'run  
pdbset' on loaded pdb files to overcome this issue?

Cheers,
Charlie

Lynn F. Ten Eyck wrote:

On 2 Oct 2008, at 09:11, Kay Diederichs wrote:

Phil Evans schrieb:
In the new coot, lots of my PDB files have all atoms coloured  
white. Is this a consequence of the new PDB format conventions

Phil


Yes I think so - I found that PDB files that behave like that lack  
the atom type in the last column (which might be req'd by the new  
PDB format convention - no idea why).
The 4-character atom name did not allow well enough for unique  
identification of the element type, especially with H atoms.   
Overloading the atom name with element type causes a lot of  
problems.  Separating the atom type to another column allows for  
both atom type and ionization state -- i.e. correct identification  
of the scattering factor needed.
Example: Atom type Fe -- is it ferrous, ferric, or ferryl?  You  
need to know for both refinement and modeling.

Lynn Ten Eyck


running through pdbset fixes this easily.

best,

Kay
--Kay Diederichs http://strucbio.biologie.uni-konstanz.de
email: [EMAIL PROTECTED] Tel +49 7531 88 4049 Fax  
3183
Fachbereich Biologie, Universitaet Konstanz, Box M647, D-78457  
Konstanz

.


--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[EMAIL PROTECTED]
+61 8 6488 4406

[COOT] OS X 10.4.X G4 ppc libgmp.3.dylib

[William G. Scott]

Does anyone have a copy of libgmp.3.dylib  from OS X 10.4.X  built on  
a G4 ppc, preferably with a single processor, that works with coot?


If so could you please email it to me?

Thanks.

Bill

Re: [COOT] CNS coordinate in COOT

[William G. Scott]

run the pdb file through ccp4's pdbset, which will canonicalize it (if  
that is a word).



On Oct 5, 2008, at 5:59 PM, Masaki UNNO wrote:


Hi Colleagues



I am using CNS for structural refinements.  I have installed  
COOT_0.5 but I
think the new version of COOT cannot display CNS coordinate  
properly.  It

did not display the color by atom and secondly structures.  How can I
display the CNS coordinate by atom or so?  The CNS version is 1.2.



Best regards.





-

Masaki Unno, PhD.



Inst. of Multidisciplinary Research for Advanced Materials,

Tohoku University



2-1-1 Katahira, Aoba, Sendai, Miyagi 980-8577, Japan

Tel: +22-217-5117

Fax: +22-217-5118

[COOT] embarrassing question

[William G. Scott]

Hi Citizens:

I can't remember who was working on pre-compiling the OS X 10.4X intel  
coot.  Could someone remind me?  Thanks, and sorry.


Bill

Re: [COOT] Nucleotide Builder

[William G. Scott]

I agree, but why do you want to build B-form RNA?

On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote:

I'm using the 'Ideal DNA/RNA...' function.  When I try to build A- 
form RNA,

I get what I want.  When I ask for B-form RNA, I get DNA!  Looks like
something to fix...

Many thanks

Re: [COOT] Nucleotide Builder

[William G. Scott]

Oh, I thought you had discovered a new form of RNA.

You might want to use phenix's elbow builder module. Then you will  
have a cif file for the ligand too.



On Oct 10, 2008, at 9:36 AM, Daniel Holloway wrote:

I'm just interested in taking one residue (a 5'-AMP or 3',5'-ADP  
with the
ribose in the C2'-endo conformation) and using it as the basis for a  
novel

ligand.

On Fri, 10 Oct 2008 09:13:57 -0700, William G. Scott
<[EMAIL PROTECTED]> wrote:


I agree, but why do you want to build B-form RNA?

On Oct 10, 2008, at 8:48 AM, Daniel Holloway wrote:


I'm using the 'Ideal DNA/RNA...' function.  When I try to build A-
form RNA,
I get what I want.  When I ask for B-form RNA, I get DNA!  Looks  
like

something to fix...

Many thanks

Re: [COOT] regarding installing coot via fink

[William G. Scott]

Dear Arnab:

kotoushu used to host 10.4 intel fink debians, but it is no longer  
available.


Since you are using 10.5, the easiest thing to do is this:


  sudo perl -pi -e  's|kotoushu|sage|g'  /sw/etc/apt/sources.list


if you need further details:  http://tinyurl.com/fink-precompiled


Also make sure you have a recent version of X11.app (ie 2.3.1):

http://xquartz.macosforge.org/trac/wiki

Bill


On Oct 14, 2008, at 7:30 AM, Arnab Bhattacharjee wrote:


Hi Bill,

This is in regard of installing coot in my Mac laptop (leopard,  
10.5). I installed the older version of coot via fink. Now I tried  
to install the latest version directly taking the pre compiled  
binaries first and then it didn't worked. Then I tried to install it  
via fink again. But repeatedly its saying


Err http://kotoushu.ucsc.edu unstable/main opensp4-shlibs 1.5.1-1006
 Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). -  
connect (61 Connection refused)

Err http://kotoushu.ucsc.edu unstable/main opensp4 1.5.1-1006
 Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). -  
connect (61 Connection refused)

Err http://kotoushu.ucsc.edu unstable/main opensp4-dev 1.5.1-1006
 Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). -  
connect (61 Connection refused)
Err http://kotoushu.ucsc.edu unstable/main sgml-entities-iso8879  
1986-4
 Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). -  
connect (61 Connection refused)

Err http://kotoushu.ucsc.edu unstable/main xft2-dev 2.1.2-5


So can u give me some tips of how to come out of the problem. I  
actually tried to overwrite the earlier version of coot and hence  
the older version doesn't work any more. Will be really helpful if u  
can bail me out of the situation.



Best regards
Arnab

Thanks and Regards
--
ARNAB BHATTACHARJEE

Dept. of Bacteriology and Immunology
SERO Group, Haartman Institute
Haartmaninkatu 3
University of Helsinki
FIN-00014 HELSINKI
Tel. +358-9-191 26385
Fax. +358-9-191 26382


Structural Biology and Biophysics
Macromolecular X-ray Crystallography Group
Institute of Biotechnology.
Biocenter: 3, Viikinkari 1
University of Helsinki
FIN-00790 HELSINKI
Tel. +358-9-191 58922
Fax  +358-9-191 59940

Re: [COOT] regarding installing coot via fink

[William G. Scott]

Hi Arnab:

Unfortunately, sometimes there are glitches installing some of these  
packages that are dependencies, and I'm not up on each of the >100  
fink dependencies that coot has.


The best thing is to try a second time, and if that doesn't work, issue

fink describe 

and it will give you an email address for the package maintainer. Also  
there is a fink user's email list with very knowledgeable people on  
it, and it is probably the fastest way to get a problem fixed.


Bill



On Oct 15, 2008, at 5:27 PM, Arnab Bhattacharjee wrote:


While installing coot via fink I am repeatedly getting this msg


/sw/bin/dpkg-lockwait -r fink-buildlock-gnome-vfs2-unified-2.20.1-2
(Reading database ... 45318 files and directories currently  
installed.)

Removing fink-buildlock-gnome-vfs2-unified-2.20.1-2 ...
Failed: phase compiling: gnome-vfs2-unified-2.20.1-2 failed


i tried to rebuid gnome-vfs2 manually as well by the rebuild and  
install command in finkcoudn't do it



Any tips plz?


Thanks and Regards
--
ARNAB BHATTACHARJEE

Dept. of Bacteriology and Immunology
SERO Group, Haartman Institute
Haartmaninkatu 3
University of Helsinki
FIN-00014 HELSINKI
Tel. +358-9-191 26385
Fax. +358-9-191 26382


Structural Biology and Biophysics
Macromolecular X-ray Crystallography Group
Institute of Biotechnology.
Biocenter: 3, Viikinkari 1
University of Helsinki
FIN-00790 HELSINKI
Tel. +358-9-191 58922
Fax  +358-9-191 59940





On 14 Oct 2008, at 20:37, William Scott wrote:


Sorry, I just realized that quick-fix won't work.

Instead, edit the file /sw/etc/apt/sources.list

take out the kotoushu lines and put in the three lines shown on  
this page:


http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Sources.list_for_10.5_intel_only

i.e.,

deb http://sage.ucsc.edu/fink_intel_10.5_only stable main crypto
deb http://sage.ucsc.edu/fink_intel_10.5_only unstable main crypto
deb http://sage.ucsc.edu/fink_intel_10.5_only local main

Then issue

fink selfupdate-rsync
sudo apt-get update
fink -b update-all


On Oct 14, 2008, at 9:43 AM, William G. Scott wrote:


Dear Arnab:

kotoushu used to host 10.4 intel fink debians, but it is no longer  
available.


Since you are using 10.5, the easiest thing to do is this:


   sudo perl -pi -e  's|kotoushu|sage|g'  /sw/etc/apt/sources.list


if you need further details:  http://tinyurl.com/fink-precompiled


Also make sure you have a recent version of X11.app (ie 2.3.1):

http://xquartz.macosforge.org/trac/wiki

Bill


On Oct 14, 2008, at 7:30 AM, Arnab Bhattacharjee wrote:


Hi Bill,

This is in regard of installing coot in my Mac laptop (leopard,  
10.5). I installed the older version of coot via fink. Now I  
tried to install the latest version directly taking the pre  
compiled binaries first and then it didn't worked. Then I tried  
to install it via fink again. But repeatedly its saying


Err http://kotoushu.ucsc.edu unstable/main opensp4-shlibs  
1.5.1-1006
Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). -  
connect (61 Connection refused)

Err http://kotoushu.ucsc.edu unstable/main opensp4 1.5.1-1006
Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). -  
connect (61 Connection refused)

Err http://kotoushu.ucsc.edu unstable/main opensp4-dev 1.5.1-1006
Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). -  
connect (61 Connection refused)
Err http://kotoushu.ucsc.edu unstable/main sgml-entities-iso8879  
1986-4
Could not connect to kotoushu.ucsc.edu:80 (128.114.150.90). -  
connect (61 Connection refused)

Err http://kotoushu.ucsc.edu unstable/main xft2-dev 2.1.2-5


So can u give me some tips of how to come out of the problem. I  
actually tried to overwrite the earlier version of coot and hence  
the older version doesn't work any more. Will be really helpful  
if u can bail me out of the situation.



Best regards
Arnab

Thanks and Regards
--
ARNAB BHATTACHARJEE

Dept. of Bacteriology and Immunology
SERO Group, Haartman Institute
Haartmaninkatu 3
University of Helsinki
FIN-00014 HELSINKI
Tel. +358-9-191 26385
Fax. +358-9-191 26382


Structural Biology and Biophysics
Macromolecular X-ray Crystallography Group
Institute of Biotechnology.
Biocenter: 3, Viikinkari 1
University of Helsinki
FIN-00790 HELSINKI
Tel. +358-9-191 58922
Fax  +358-9-191 59940

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Since Ubuntu has gotten to be popular (for good reason, IMO), it might be
useful to have an official (or at least semi-official) debian package whose
installation would guarantee all the dependencies also get installed.  I've
tried to do it in a half-arsed sort of way, but lately have dropped the ball
(sorry).
On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan <[EMAIL PROTECTED]>wrote:

> Hi!
>
> Firstly, do you need to build coot at all? There are binary packages which
> work just fine on Gutsy. You can install them wherever you want on your
> system, and they should just work.
>
> Secondly, if for some reason you do want to build your own (you want to
> make changes to the code???), then are you using the build-it-gtk2-simple
> script?
>
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
> Building coot without this script requires days or weeks of messing around
> with dependencies. With this script it is usually pretty easy.
>
> Kevin
>
>
> Rimi wrote:
>
>> Hi all,
>>  I am new to coot. Recently I tried to install coot in my ubuntu
>> gutsy. But it can not find mmdb library somehow. Below is the message
>>
>


-- 
-


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

Please reply to:  [EMAIL PROTECTED]

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Hi Mark et al:

The last coot I compiled on Ubuntu Hardy was coot-0.5-pre-1- 
revision-1003.  I've been a bit distracted with other obligations. The  
last one I made into a debian package and put on our server was a
0.4-pre-2release, so I apologize. I keep the OS X fink debian  
packages much more up to date and have tried to maintain those,  
officially (via fink), to a much higher standard.


I don't fully understand the linux debian packaging requirements  
nearly well enough, but should probably take the time to do so, and to  
create standard-compliant debian packages for coot and its  
dependencies and then figure out how to get these things into the  
official distribution system.  I guess if someone else out there with  
the competence and time can do for Debian/Ubuntu what Donnie Berkholz  
has done for Gentoo, it would be helpful.  What is needed are properly  
created debian packages for clipper, mmdb, gpp4, ssm, coot, and a few  
of the other misc dependencies that aren't present in a standard linux  
distribution.


Once you have that, you can use the program alien to convert to rpm,  
etc.


My main limitations are knowledge, time, only one PC running only one  
version of ubuntu, and more specifically getting a complete listing of  
dependencies so that package installation for the end-user is truly  
seamless.  This has been my goal with OSX/fink, and I've invested most  
of my time and effort into that. Linux should actually be much easier,  
but I don't know it nearly as well. I've also now just been put into a  
tailspin by our main funding agency, so I will now have to prioritize  
further, or find something else to do for a living.


Peace and joy,

Bill




On Nov 15, 2008, at 3:32 AM, Mark Brooks wrote:


Hi,

It may be useful to have a 'contrib' section for the Coot binary  
download
web page (or even some unofficial web page), so that we have more  
options of
binaries to test. For example, upon upgrading to Ubuntu Hardy Heron,  
Coot

stopped working, for reasons beyond my understanding, but worked when
recompiled. (Which was very easy using the build-it-gtk2-simple  
script BTW).
To have a central repository of tested binaries could be very handy,  
to

avoid having to do this.

The Coot developers and yourself (Bill) have done an enormous amount  
to

furnish us with working, tested programs,  but perhaps one or two more
updated binaries contributed by users  would be useful, especially  
for newer

releases of the myriad Linux flavours.

I think for the Coot developers to start providing .deb, .rpm and  
Gentoo
packages for every update is too onerous, especially when .tar.gz  
files work

OK. Just my opinion.

Which Ubuntu are you on Bill, and which binary are you using? Are  
these on
your debian web site? I guess I may be able to give a Hardy Heron  
binary if

need be.

Thanks for your .debs though, I use them all the time.

Mark

2008/11/12 William G. Scott <[EMAIL PROTECTED]>

Since Ubuntu has gotten to be popular (for good reason, IMO), it  
might be
useful to have an official (or at least semi-official) debian  
package whose
installation would guarantee all the dependencies also get  
installed.  I've
tried to do it in a half-arsed sort of way, but lately have dropped  
the ball

(sorry).

On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan  
<[EMAIL PROTECTED]>wrote:



Hi!

Firstly, do you need to build coot at all? There are binary  
packages which
work just fine on Gutsy. You can install them wherever you want on  
your

system, and they should just work.

Secondly, if for some reason you do want to build your own (you  
want to
make changes to the code???), then are you using the build-it-gtk2- 
simple

script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
Building coot without this script requires days or weeks of  
messing around

with dependencies. With this script it is usually pretty easy.

Kevin


Rimi wrote:


Hi all,
I am new to coot. Recently I tried to install coot in my  
ubuntu
gutsy. But it can not find mmdb library somehow. Below is the  
message







--
-------------


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott<http://chemistry.ucsc.edu/%7Ewgscott 
>


Please reply to:  [EMAIL PROTECTED]







--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

That's great.  In the short term, highly unofficial/unauthorized/ 
zeroth-order coot and dependencies for i386 linux:


debians:

<http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files 
>


rpms (made via alien from above):

<http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages 
>


These include mmdb, ssm, gpp4, fftw (in the form required for clipper  
and coot), clipper, coot, which will install into /usr/local/xtal


and then the various guile-type dependencies, which will install into / 
usr



On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:

FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on  
crystallographic libs for Ubuntu, e.g.:


https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb

When he gets round to Coot I'm keen to help make his life easier.

Regards,

Paul.


Mark Brooks wrote:

Hi,
It may be useful to have a 'contrib' section for the Coot binary  
download web page (or even some unofficial web page), so that we  
have more options of binaries to test. For example, upon upgrading  
to Ubuntu Hardy Heron, Coot stopped working, for reasons beyond my  
understanding, but worked when recompiled. (Which was very easy  
using the build-it-gtk2-simple script BTW). To have a central  
repository of tested binaries could be very handy, to avoid having  
to do this.
The Coot developers and yourself (Bill) have done an enormous  
amount to furnish us with working, tested programs,  but perhaps  
one or two more updated binaries contributed by users  would be  
useful, especially for newer releases of the myriad Linux flavours.
I think for the Coot developers to start providing .deb, .rpm and  
Gentoo packages for every update is too onerous, especially  
when .tar.gz files work OK. Just my opinion.
Which Ubuntu are you on Bill, and which binary are you using? Are  
these on your debian web site? I guess I may be able to give a  
Hardy Heron binary if need be.

Thanks for your .debs though, I use them all the time.
Mark
2008/11/12 William G. Scott <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED] 
>>

   Since Ubuntu has gotten to be popular (for good reason, IMO), it
   might be useful to have an official (or at least semi-official)
   debian package whose installation would guarantee all the
   dependencies also get installed.  I've tried to do it in a
   half-arsed sort of way, but lately have dropped the ball  
(sorry). On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan

   <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
   Hi!
   Firstly, do you need to build coot at all? There are binary
   packages which work just fine on Gutsy. You can install them
   wherever you want on your system, and they should just work.
   Secondly, if for some reason you do want to build your own  
(you

   want to make changes to the code???), then are you using the
   build-it-gtk2-simple script?
   
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
   Building coot without this script requires days or weeks of
   messing around with dependencies. With this script it is  
usually

   pretty easy.
   Kevin
   Rimi wrote:
   Hi all,
I am new to coot. Recently I tried to install  
coot

   in my ubuntu
   gutsy. But it can not find mmdb library somehow. Below is
   the message
   --  
---------

   William G. Scott
   contact info:  http://chemistry.ucsc.edu/~wgscott
   <http://chemistry.ucsc.edu/%7Ewgscott>
   Please reply to:  [EMAIL PROTECTED]
   <mailto:[EMAIL PROTECTED]>
--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Woops.  I didn't see that.  I auto-generated the list of dependencies  
from the output of ldd on the coot binary, upon which I then used dpgk  
-S to find the corresponding packages. For some reason it generated  
this falsely (the library is also present, but ldd does not report  
coot linking anything with NX in the path).


Sorry, I will edit this out.

Thanks for testing.

Bill



On Nov 17, 2008, at 3:16 AM, Mark Brooks wrote:


Hi,

I just tested it on a freshly installed system for a student; it  
works very

well on Ubuntu Hardy.

I'm not sure why "nxnode" is a dependency of the Coot .deb though!  
(Although

that doesn't bother me too much- I would advise anyone to use NX ).

Thanks again,

Mark

2008/11/16 William G. Scott <[EMAIL PROTECTED]>


That's great.  In the short term, highly
unofficial/unauthorized/zeroth-order coot and dependencies for i386  
linux:


debians:

<
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files




rpms (made via alien from above):

<
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages




These include mmdb, ssm, gpp4, fftw (in the form required for  
clipper and

coot), clipper, coot, which will install into /usr/local/xtal

and then the various guile-type dependencies, which will install  
into /usr




On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:

FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on

crystallographic libs for Ubuntu, e.g.:

https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb

When he gets round to Coot I'm keen to help make his life easier.

Regards,

Paul.


Mark Brooks wrote:


Hi,
It may be useful to have a 'contrib' section for the Coot binary  
download
web page (or even some unofficial web page), so that we have more  
options of
binaries to test. For example, upon upgrading to Ubuntu Hardy  
Heron, Coot
stopped working, for reasons beyond my understanding, but worked  
when
recompiled. (Which was very easy using the build-it-gtk2-simple  
script BTW).
To have a central repository of tested binaries could be very  
handy, to

avoid having to do this.
The Coot developers and yourself (Bill) have done an enormous  
amount to
furnish us with working, tested programs,  but perhaps one or two  
more
updated binaries contributed by users  would be useful,  
especially for newer

releases of the myriad Linux flavours.
I think for the Coot developers to start providing .deb, .rpm and  
Gentoo
packages for every update is too onerous, especially when .tar.gz  
files work

OK. Just my opinion.
Which Ubuntu are you on Bill, and which binary are you using? Are  
these
on your debian web site? I guess I may be able to give a Hardy  
Heron binary

if need be.
Thanks for your .debs though, I use them all the time.
Mark
2008/11/12 William G. Scott <[EMAIL PROTECTED] >
 Since Ubuntu has gotten to be popular (for good reason, IMO), it
 might be useful to have an official (or at least semi-official)
 debian package whose installation would guarantee all the
 dependencies also get installed.  I've tried to do it in a
 half-arsed sort of way, but lately have dropped the ball (sorry).
On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan
 <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
 Hi!
 Firstly, do you need to build coot at all? There are binary
 packages which work just fine on Gutsy. You can install them
 wherever you want on your system, and they should just work.
 Secondly, if for some reason you do want to build your own  
(you

 want to make changes to the code???), then are you using the
 build-it-gtk2-simple script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
 Building coot without this script requires days or weeks of
 messing around with dependencies. With this script it is  
usually

 pretty easy.
 Kevin
 Rimi wrote:
 Hi all,
  I am new to coot. Recently I tried to install  
coot

 in my ubuntu
 gutsy. But it can not find mmdb library somehow. Below is
 the message
 --
---------
 William G. Scott
 contact info:  http://chemistry.ucsc.edu/~wgscott<http://chemistry.ucsc.edu/%7Ewgscott 
>

 <http://chemistry.ucsc.edu/%7Ewgscott>
 Please reply to:  [EMAIL PROTECTED]
 <mailto:[EMAIL PROTECTED]>
--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks






--
Mark BROOKS
Telephone: 0169157968
Fax: 0169853715
Institut de Biochmie et de Biophysique Moleculaire et Cellulaire
UMR8619 - Bât 430 - Université de Paris-Sud
91405 Orsay CEDEX
Skype: markabrooks

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

Oh, in case anyone is wondering how I did this (and how I screwed it  
up), the correct command should have been:


dpkg -S $(  ldd /usr/local/xtal/coot/bin/coot-real | awk '{print $3}'  
| sort -u | grep -v \(  )| cut -f 1 -d ":" | sort -u | perl -pi -e 's| 
\n|\, |g' >| dependencies.txt


whereas I first used

dpkg -S $(  ldd /usr/local/xtal/coot/bin/coot-real | awk '{print $1}'  
| sort -u | grep -v \(  )| cut -f 1 -d ":" | sort -u | perl -pi -e 's| 
\n|\, |g' >| dependencies.txt


My bad.  I needed the third column of the output of ldd to get the  
full path of the dynamic library. The first column only reports the  
name of the file, and then it wrongly assumed it was in my NX  
directory (it wasn't). Coot was properly linked. The list of  
dependencies in the debian file was wrong. Fixed now.   
( coot_0.5-2_i386.deb ).  Again, thanks for catching this.


Bill



On Nov 17, 2008, at 6:57 AM, William G. Scott wrote:

Woops.  I didn't see that.  I auto-generated the list of  
dependencies from the output of ldd on the coot binary, upon which I  
then used dpgk -S to find the corresponding packages. For some  
reason it generated this falsely (the library is also present, but  
ldd does not report coot linking anything with NX in the path).


Sorry, I will edit this out.

Thanks for testing.

Bill



On Nov 17, 2008, at 3:16 AM, Mark Brooks wrote:


Hi,

I just tested it on a freshly installed system for a student; it  
works very

well on Ubuntu Hardy.

I'm not sure why "nxnode" is a dependency of the Coot .deb though!  
(Although

that doesn't bother me too much- I would advise anyone to use NX ).

Thanks again,

Mark

2008/11/16 William G. Scott <[EMAIL PROTECTED]>


That's great.  In the short term, highly
unofficial/unauthorized/zeroth-order coot and dependencies for  
i386 linux:


debians:

<
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Instalation_on_Debian.2FUbuntu_from_debian_archive_files




rpms (made via alien from above):

<
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Converting_to_rpm_packages




These include mmdb, ssm, gpp4, fftw (in the form required for  
clipper and

coot), clipper, coot, which will install into /usr/local/xtal

and then the various guile-type dependencies, which will install  
into /usr




On Nov 15, 2008, at 6:15 PM, Paul Emsley wrote:

FYI, IIUC, Morten Kjeldgaard has become a MOTU and is working on

crystallographic libs for Ubuntu, e.g.:

https://launchpad.net/ubuntu/+source/clipper
https://launchpad.net/ubuntu/+source/mmdb

When he gets round to Coot I'm keen to help make his life easier.

Regards,

Paul.


Mark Brooks wrote:


Hi,
It may be useful to have a 'contrib' section for the Coot binary  
download
web page (or even some unofficial web page), so that we have  
more options of
binaries to test. For example, upon upgrading to Ubuntu Hardy  
Heron, Coot
stopped working, for reasons beyond my understanding, but worked  
when
recompiled. (Which was very easy using the build-it-gtk2-simple  
script BTW).
To have a central repository of tested binaries could be very  
handy, to

avoid having to do this.
The Coot developers and yourself (Bill) have done an enormous  
amount to
furnish us with working, tested programs,  but perhaps one or  
two more
updated binaries contributed by users  would be useful,  
especially for newer

releases of the myriad Linux flavours.
I think for the Coot developers to start providing .deb, .rpm  
and Gentoo
packages for every update is too onerous, especially  
when .tar.gz files work

OK. Just my opinion.
Which Ubuntu are you on Bill, and which binary are you using?  
Are these
on your debian web site? I guess I may be able to give a Hardy  
Heron binary

if need be.
Thanks for your .debs though, I use them all the time.
Mark
2008/11/12 William G. Scott <[EMAIL PROTECTED] >
Since Ubuntu has gotten to be popular (for good reason, IMO), it
might be useful to have an official (or at least semi-official)
debian package whose installation would guarantee all the
dependencies also get installed.  I've tried to do it in a
half-arsed sort of way, but lately have dropped the ball (sorry).
On Wed, Nov 12, 2008 at 1:03 AM, Kevin Cowtan
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
Hi!
Firstly, do you need to build coot at all? There are binary
packages which work just fine on Gutsy. You can install them
wherever you want on your system, and they should just work.
Secondly, if for some reason you do want to build your own  
(you

want to make changes to the code???), then are you using the
build-it-gtk2-simple script?

http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installation_from_source_code
Building coot without this script requires days or weeks of
messing around with dependenci

Re: [COOT] problem in loading icons

[William G. Scott]

Hi Enrico:

I have this:

% dpkg -S svg_loader.so
librsvg2-gtk: /sw/lib/gtk-2.0/2.10.0/loaders/svg_loader.so

The package that provides this is librsvg2-gtk, which should be a coot  
dependency.


Could you please check, and maybe try reinstalling it, ie.

fink reinstall librsvg2-gtk

and let me know what happens?

Many thanks in advance, and also many thanks to Charles Ballard for  
pointing this out.


Bill




On Nov 17, 2008, at 12:49 PM, Ballard, CC (Charles) wrote:


Hi Enrico

For some reason the pixbuf.loaders file does not contain the  
information

about the svg_loader.  This is normally achieved by running
gdk-pixbuf-query-loaders and piping the output to the pixbuf.loaders
file (use find to locate it).  To confirm that you have the svg  
library

setup in gdk in the first place try and locate the svg_loader.la file
(in my case - none fink - it is in lib/gtk-2.0/2.10.0/loaders ).
gdk-pixbuf-query-loaders will have a manual page if more info is
required.

If all else fails, there is a bundle of coot 0.5 at
http://www.ccp4.ac.uk/download/downloadman.php

Charles

-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:[EMAIL PROTECTED] On Behalf Of Enrico Malito
Sent: 17 November 2008 16:09
To: COOT@JISCMAIL.AC.UK
Subject: [COOT] problem in loading icons

Hello,

I was wondering if anybody observed this before. When I start coot I  
get
this messages (a long list of errors for the whole content of the  
folder

/sw/share/coot/pixmaps/):

Error loading icon: Couldn't recognize the image file format for file
'/sw/share/coot/pixmaps/add-alt-conf.svg'
Error loading icon: Couldn't recognize the image file format for file
'/sw/share/coot/pixmaps/add-peptide-1.svg'
...
...
Error loading icon: Couldn't recognize the image file format for file
'/sw/share/coot/pixmaps/undo-1.png'
Error loading icon: Couldn't recognize the image file format for file
'/sw/share/coot/pixmaps/unknown-blob.png'
initalize graphics molecules...done.

and no icons are loaded in the right bar of coot, only grey boxes (see
attach).
This is 0.5.1-pre-1 installed through fink on OSX 10.5.5, and those
icons files are actually there (in /sw/share/coot/pixmaps/) and seem  
oK.


Thanks much in advance for any hints.
EM

Re: [COOT] problem in loading icons

[William G. Scott]

Another idea:

If you have $DYLD_LIBRARY_PATH assigned, try unsetting it before  
invoking coot, i.e., issue


DYLD_LIBRARY_PATH=""  ; coot


On Nov 17, 2008, at 8:09 AM, Enrico Malito wrote:


Hello,

I was wondering if anybody observed this before. When I start coot I  
get this messages (a long list of errors for the whole content of  
the folder /sw/share/coot/pixmaps/):


Error loading icon: Couldn't recognize the image file format for  
file '/sw/share/coot/pixmaps/add-alt-conf.svg'
Error loading icon: Couldn't recognize the image file format for  
file '/sw/share/coot/pixmaps/add-peptide-1.svg'

...
...
Error loading icon: Couldn't recognize the image file format for  
file '/sw/share/coot/pixmaps/undo-1.png'
Error loading icon: Couldn't recognize the image file format for  
file '/sw/share/coot/pixmaps/unknown-blob.png'

initalize graphics molecules...done.

and no icons are loaded in the right bar of coot, only grey boxes  
(see attach).
This is 0.5.1-pre-1 installed through fink on OSX 10.5.5, and those  
icons files are actually there (in /sw/share/coot/pixmaps/) and seem  
oK.


Thanks much in advance for any hints.
EM

Re: [COOT] problem in coot installation in ubuntu

[William G. Scott]

On Nov 18, 2008, at 6:26 PM, Tim Fenn wrote:


The reason I bring up the guile dependencies in particular is they're
the only tricky part in getting rpms made, since without an upstream,
they're unlikely to get accepted.  Otherwise I'd be happy to  
contribute

those as well to fedora.



Create a distraction and sneak them in.

http://diablo.ucsc.edu/~wgscott/debian/rpm/coot/dependencies/

But seriously, if they are GPL-ed, why not just stick them in coot's  
scheme directory and be done with it?

Re: [COOT] problem in loading icons

[William G. Scott]

I just finally managed to replicate the problem.

If I start a bash shell without sourcing /sw/bin/init.sh to set up the  
fink environment, I get this problem too.


So first issue

source /sw/bin/init.sh

then

coot

(or if you use tcsh, issue "source /sw/bin/init.csh ).

This not only sets up the $PATH, but ensures the rest of the  
environment is set up correctly by sourcing the various files in the  
directory /sw/etc/profile.d





On Nov 18, 2008, at 12:10 PM, Enrico Malito wrote:


Dear Dr. Scott,
thanks for your messages.

I've tried both your suggestions, but they did not help.

I do have:

% dpkg -S svg_loader.so
librsvg2-gtk: /sw/lib/gtk-2.0/2.10.0/loaders/svg_loader.so

tried to fink reinstall librsvg2-gtk, here what I get:

Information about 7428 packages read in 6 seconds.
The following package will be reinstalled:
librsvg2-gtk
Reading buildlock packages...
/sw/bin/dpkg-lockwait -i /sw/var/cache/apt/archives/librsvg2- 
gtk_2.22.3-1_darwin-i386.deb
(Reading database ... 36662 files and directories currently  
installed.)
Preparing to replace librsvg2-gtk 2.22.3-1 (using .../librsvg2- 
gtk_2.22.3-1_darwin-i386.deb) ...

Unpacking replacement librsvg2-gtk ...
Setting up librsvg2-gtk (2.22.3-1) ...

and also tried DYLD_LIBRARY_PATH=""  ; coot

Unfortunately I am still having the same problem.
E.




On Nov 17, 2008, at 5:52 PM, William G. Scott wrote:


Hi Enrico:

I have this:

% dpkg -S svg_loader.so
librsvg2-gtk: /sw/lib/gtk-2.0/2.10.0/loaders/svg_loader.so

The package that provides this is librsvg2-gtk, which should be a  
coot dependency.


Could you please check, and maybe try reinstalling it, ie.

fink reinstall librsvg2-gtk

and let me know what happens?

Many thanks in advance, and also many thanks to Charles Ballard for  
pointing this out.


Bill




On Nov 17, 2008, at 12:49 PM, Ballard, CC (Charles) wrote:


Hi Enrico

For some reason the pixbuf.loaders file does not contain the  
information

about the svg_loader.  This is normally achieved by running
gdk-pixbuf-query-loaders and piping the output to the pixbuf.loaders
file (use find to locate it).  To confirm that you have the svg  
library
setup in gdk in the first place try and locate the svg_loader.la  
file

(in my case - none fink - it is in lib/gtk-2.0/2.10.0/loaders ).
gdk-pixbuf-query-loaders will have a manual page if more info is
required.

If all else fails, there is a bundle of coot 0.5 at
http://www.ccp4.ac.uk/download/downloadman.php

Charles

-Original Message-
From: Mailing list for users of COOT Crystallographic Software
[mailto:[EMAIL PROTECTED] On Behalf Of Enrico Malito
Sent: 17 November 2008 16:09
To: COOT@JISCMAIL.AC.UK
Subject: [COOT] problem in loading icons

Hello,

I was wondering if anybody observed this before. When I start coot  
I get
this messages (a long list of errors for the whole content of the  
folder

/sw/share/coot/pixmaps/):

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

'/sw/share/coot/pixmaps/add-alt-conf.svg'
Error loading icon: Couldn't recognize the image file format for  
file

'/sw/share/coot/pixmaps/add-peptide-1.svg'
...
...
Error loading icon: Couldn't recognize the image file format for  
file

'/sw/share/coot/pixmaps/undo-1.png'
Error loading icon: Couldn't recognize the image file format for  
file

'/sw/share/coot/pixmaps/unknown-blob.png'
initalize graphics molecules...done.

and no icons are loaded in the right bar of coot, only grey boxes  
(see

attach).
This is 0.5.1-pre-1 installed through fink on OSX 10.5.5, and those
icons files are actually there (in /sw/share/coot/pixmaps/) and  
seem oK.


Thanks much in advance for any hints.
EM

Re: [COOT] coot crash upon ncs ghost display

[William G. Scott]

I'll remake the others if using the most current version is all that  
is needed.



On Dec 11, 2008, at 12:47 AM, Miguel Ortiz Lombardia wrote:


Dear Valerie, Paul and others,

FWIW, rather interestingly, we don't observe this crash on:

Intel-Mac OS X.5.5
Coot 0.5.1-pre-1 rev. 1626
Bill's fink build

All SSM seems to work all right, including superposing one of the  
monomers on top of another one (by moving a copy of the molecule)


Best regards,


Miguel

Le 11 Dec 2008 à 09:25, Paul Emsley a écrit :


Valerie Biou wrote:

Hello
I have coot v. 0.5 with macosx 10.5.5 with an intel processor.  
Each time I

try to display the ncs ghost coot crashes. Is this a known problems?


Dear Valerie,

That sounds bad, and yes, I think there is a known problem of using  
SSM (which is what 0.5 uses to generate the ghost matrices) on mac  
in Bill's 0.5 build :-(  There is no work-around that I know of in  
0.5.


One day, I hope to have the skills to build Coot on Mac myself  
(that day seems a long way off...)


In recent 0.5.1 pre-releases you can use NCS Residue Range to make  
the matrices using LSQ.


Paul.

--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.



--
Miguel Ortiz Lombardía
!!!
!!!  NEW ADDRESS!!!
!!!
Architecture et Fonction des Macromolécules Biologiques
UMR6098, CNRS, Université Aix-Marseille I & II
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: [EMAIL PROTECTED]
Web: http://www.pangea.org/mol/spip.php?rubrique2


--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [COOT] coot crash upon ncs ghost display

[William G. Scott]

On Dec 11, 2008, at 12:25 AM, Paul Emsley wrote:



One day, I hope to have the skills to build Coot on Mac myself (that  
day seems a long way off...)


Nonsense.  Come to California for a visit, and we'll have it going in  
no time.  (I'd come to balmy ol' England, but I'm under US State  
Department travel restrictions for wanton deployment of sarcasm  
against the current administration.)

[COOT] OSX: pre-compiled stand-alone coot-0.5.1-pre1 for 10.4 AND 10.5 available courtesy of Geoff Franks

[William G. Scott]

Dear Mac OSX coot users:

Here is a recent 0.5.1-pre1 pre-compiled version of coot and  
instructions to download (185 MB) and to install it:


http://tinyurl.com/intelcoot10-4-10-5

Many thanks to Geoff Franks, (Sr. Systems Administrator, Hauptman  
Woodward Institute), who compiled this for the community!!!


I'll have a G5 ppc 10.5 version available at the same site within the  
next few hours.


**Please Note**
If you have a working fink version of coot, there is no need to  
download this.  It is the exact same thing, except everything is built  
in /usr/local/xtal/coot instead of /sw.


Peace and Joy,

Bill


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

Re: [COOT] coot for 10.4 and 10.5 intel

[William G. Scott]

If you have a ~/.gtkrc-2.0  file, try moving this out of the way or  
deleting font specifications.

On Dec 11, 2008, at 3:38 AM, Antony Oliver wrote:



(coot-real:42412): Pango-WARNING **: Error loading GDEF table 28333
(coot-real:42412): Pango-WARNING **: Error loading GSUB table 28333
(coot-real:42412): Pango-WARNING **: Error loading GPOS table 28333
initalize graphics molecules...done.
---

Re: [COOT] coot for 10.4 and 10.5 intel

[William G. Scott]

The only difference should be the version of coot.


On Dec 15, 2008, at 10:23 AM, Nathaniel Echols wrote:

Hey Bill, this has the correct and complete Python module search  
paths too
(although /usr/local/xtal/coot/share/coot/python is repeated four  
times, but
this doesn't appear to break anything).  What's the difference  
between this

and the coot-0.5-pre1 build you sent out on Thursday?
thanks,
Nat

(still no coot_python, but I'm pretty sure that's a different  
problem.)


On Fri, Dec 12, 2008 at 9:40 PM, William Scott
wrote:


Is this one any better?


http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Coot-0.5.1-pre1_revision_1661_for_intel-10.4-10.5



On Fri, December 12, 2008 2:53 am, Valerie Biou wrote:

Hi Bill,

I installed it this morning and it starts ok. all I tried is SSM, it

still

crashes. Do you want me to test other things?
all the best

Valerie






William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/

Re: [COOT] Glossy_P gtk+2

[William G. Scott]

That would be my fault.

On Ubuntu, I have this:

% more /etc/gtk-2.0/gtkrc

include "/usr/share/themes/Glossy\ P/gtk-2.0/gtkrc"
gtk-font-name = "Sans 13"

The one difference I see is the escaped space rather than the  
underscore, so verify which you should have.




On Jan 16, 2009, at 8:30 AM, Stefan Arold wrote:


Dear All,

I am using coot 0.5.2 on a PC (i686 Intel(R) Core(TM)2 Duo 2.20GHz
GNU/Linux) under mandriva 2008.
I tried to install the Glossy_P gtk +2 themes as described in the  
coot wiki.



To get this effect, you need the Glossy_P gtk+2 theme:
http://art.gnome.org/download/themes/gtk2/571/GTK2-Glossy_P.tar.gz
Edit a file called ~/.gtkrc-2.0 and put into it the following line:
include "/usr/share/themes/Glossy_P/gtk-2.0/gtkrc"


However: no effect...
I've tried to copy the Glossy_P/gtk-2.0/gtkrc in various places,  
including

the subdirectories 'themes' and 'etc' of my current coot download
(coot-Linux-i386-redhat-8.0-gtk1-python). Without effect...

any help to gloss my coot would be greatly appreciated!
Cheers
Stefan

Re: [COOT] Glossy_P gtk+2

[William G. Scott]

Convention is to put it in /usr/share/themes  but it can go anywhere.   
You can source it systemwide with


/etc/gtk-2.0/gtkrc

and the include line should have the absolute path in double quotes

Alternatively, you can source the file from

~/.gtkrc-2.0

and it should work.

Or if you use gnome, just download the tarball and install the theme  
by pointing the gnome theme manager to the tarball.  Similarly with  
xfce4.  I don't know how it works on KDE.


It will change all the gkt+2 stuff, not just coot.

On Jan 16, 2009, at 9:36 AM, Stefan Arold wrote:


Thank you for your swift reply!

Anticipating problems with the space in the name, I had initially  
changed the directory name to Glossy_P (-no space). However,  
changing it back, and pointing to it in the way you indicated, does  
not help...

Is there a particular directory where Glossy P needs to be sitting?
Or where the  .gtkrc-2.0 file (containing the include "/usr/share/ 
themes/Glossy\ P/gtk-2.0/gtkrc") needs to be placed? (I tried ~/, or  
COOT subdirectories etc and themes)
Or did I miss out something in my path? (for COOT it points at the  
bin directory of the current COOT download)


Many thanks for your time and suggestions!
Stefan



==
Stefan T. Arold, PhD
Centre de Biochimie Structurale
CNRS UMR 5048 - UM 1 - INSERM UMR 554
29 rue de Navacelles
34090 MONTPELLIER Cedex  - France
email: stefan.ar...@cbs.cnrs.fr
Phone: +33 (0)4.67.41.77.02
Fax:   +33 (0)4.67.41.79.13
==

- Original Message - From: "William G. Scott" >

To: 
Sent: Friday, January 16, 2009 6:04 PM
Subject: Re: Glossy_P gtk+2



That would be my fault.

On Ubuntu, I have this:

% more /etc/gtk-2.0/gtkrc

include "/usr/share/themes/Glossy\ P/gtk-2.0/gtkrc"
gtk-font-name = "Sans 13"

The one difference I see is the escaped space rather than the   
underscore, so verify which you should have.




On Jan 16, 2009, at 8:30 AM, Stefan Arold wrote:


Dear All,

I am using coot 0.5.2 on a PC (i686 Intel(R) Core(TM)2 Duo 2.20GHz
GNU/Linux) under mandriva 2008.
I tried to install the Glossy_P gtk +2 themes as described in the   
coot wiki.



To get this effect, you need the Glossy_P gtk+2 theme:
http://art.gnome.org/download/themes/gtk2/571/GTK2-Glossy_P.tar.gz
Edit a file called ~/.gtkrc-2.0 and put into it the following line:
include "/usr/share/themes/Glossy_P/gtk-2.0/gtkrc"


However: no effect...
I've tried to copy the Glossy_P/gtk-2.0/gtkrc in various places,  
including

the subdirectories 'themes' and 'etc' of my current coot download
(coot-Linux-i386-redhat-8.0-gtk1-python). Without effect...

any help to gloss my coot would be greatly appreciated!
Cheers
Stefan

[COOT] python and coot question

[William G. Scott]

Hi citizens:

OS X comes with a version of python that doesn't play well with x- 
windows-based modules, so when compiling and running coot, I would  
like to make sure that I use a different version of python that has  
things like the gtk2 modules in its sys.path.  However, despite having  
the other python (/sw/bin/python) at the head of my $PATH, the system  
python seems to be embedded in coot's interpreter, at least from what  
I can see:


This is what I want:

zsh-% which python
/sw/bin/python

zsh-% python
Python 2.6 (r26:66714, Nov  2 2008, 12:54:49)
[GCC 4.0.1 (Apple Inc. build 5484)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sys
>>> print sys.path
['', '/sw/lib/python26.zip', '/sw/lib/python2.6', '/sw/lib/python2.6/ 
plat-darwin', '/sw/lib/python2.6/plat-mac', '/sw/lib/python2.6/plat- 
mac/lib-scriptpackages', '/sw/lib/python2.6/lib-tk', '/sw/lib/ 
python2.6/lib-old', '/sw/lib/python2.6/lib-dynload', '/sw/lib/ 
python2.6/site-packages', '/sw/lib/python2.6/site-packages/Numeric', '/ 
sw/lib/python2.6/site-packages/gtk-2.0']

>>>


But with coot, I think it is using /usr/bin/python, because I get this:

COOT_PYTHON_DIR was defined to be /sw/share/coot/python
  but no PyGtk and hence no coot_gui.
Entry contents: print sys.path
Running string: print sys.path
['/System/Library/Frameworks/Python.framework/Versions/2.5/lib/ 
python25.zip', '/System/Library/Frameworks/Python.framework/Versions/ 
2.5/lib/python2.5', '/System/Library/Frameworks/Python.framework/ 
Versions/2.5/lib/python2.5/plat-darwin', '/System/Library/Frameworks/ 
Python.framework/Versions/2.5/lib/python2.5/plat-mac', '/System/ 
Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/plat- 
mac/lib-scriptpackages', '/System/Library/Frameworks/Python.framework/ 
Versions/2.5/Extras/lib/python', '/System/Library/Frameworks/ 
Python.framework/Versions/2.5/lib/python2.5/lib-tk', '/System/Library/ 
Frameworks/Python.framework/Versions/2.5/lib/python2.5/lib-dynload', '/ 
Library/Python/2.5/site-packages', '/System/Library/Frameworks/ 
Python.framework/Versions/2.5/Extras/lib/python/PyObjC', '/sw/share/ 
coot/python', '/sw/share/coot/python', '/sw/share/coot/python', '/sw/ 
share/coot/python']


which is the same sys.path I get for /usr/bin/python, apart from the  
last four redundant entries.


How do I deal with this?


Bill

Re: [COOT] python and coot question

[William G. Scott]

On Jan 30, 2009, at 10:50 AM, Nathaniel Echols wrote:


the binaries I was using of coot-0.5-pre1
had this problem, while coot-0.5.1-pre1-1661 used the correct  
interpreter.



That sounds like something I made, in which case I am even more puzzled.


The interpreter is actually supposed to be coot itself - I don't think
/sw/bin/python is going to do you any good, since it doesn't have  
access to

the memory of the running coot process.


OK, but somewhere coot is making the decision to use the system's  
python libraries in sys.path, so I am assuming it can only get these  
from /usr/bin/python.


I think if I can consistently get it to use /sw/bin/python, then at  
least I will know what I am trying to fix.

Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1

[William G. Scott]

Hi Engin:

Well, I have to confess I only tested it with zsh and tcsh, assuming  
bash would work the same way.  zsh is vastly better than bash, but you  
are right, it should work equally well on whichever shell the user  
chooses.


So I initiated a bash session, no $PYTHONPATH defined,

then

  source /sw/bin/init.sh

and then issued

   coot

and it works.

If you don't source /sw/bin/init.sh, it won't work, and many other  
things in fink will be broken.  That is the only thing I can think of.  
Sorry if that isn't relevant.


Are you on 10.4?  I don't have access to 10.4 at the moment to test  
it...


Bill







On Feb 5, 2009, at 7:50 PM, Engin Ozkan wrote:


Hi everyone,

I still seem to have issues with fink'ed coot (revision-1847-1). It  
does not start and it gives an error

PYTHONPATH: Undefined variable.

I guess I could just define the PYTHONPATH, but I do not have a  
reason to. More interestingly, if I switch to zsh shell, I don't get  
the error and coot starts, even though I still don't have the  
variable defined.


Am I missing something here?

Thanks,

Engin

William Scott wrote:

Howdie Fulica aficionados:

coot-0.6-pre-1-revision-1847-1, available via fink (and my servers  
as binaries for 10.5), should be working properly now with  
python2.5.  It should also inherit $PYTHONPATH from your  
environment if you have set that (there is generally no need to,  
but you may have a reason).


HTH,

Bill

Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1

[William G. Scott]

I just discovered that too:

tcsh-% coot
DISPLAY has been set to /tmp/launch-Oj1wSR/:0
PYTHONPATH: Undefined variable.
tcsh-%

The problem is really in /sw/bin/coot

Edit that file (it is now a wrapper script)  and get rid of the  
spurious \ in the first line.  This is the real cause of the problem.


zsh and bash apparently cope with it because they are sh-type shells.

Sorry, and thanks for finding that problem.

Bill




On Feb 5, 2009, at 8:30 PM, Engin Ozkan wrote:

I am sorry, I forgot to mention, I was actually using tcsh, not  
bash. And I do have /sw/bin/init.csh source'd (Fink-related  
everything else seems to work fine anyway).


Thanks for looking into it (and maintaining the fink packages).

Engin

William G. Scott wrote:

Hi Engin:

Well, I have to confess I only tested it with zsh and tcsh,  
assuming bash would work the same way.  zsh is vastly better than  
bash, but you are right, it should work equally well on whichever  
shell the user chooses.


So I initiated a bash session, no $PYTHONPATH defined,

then

 source /sw/bin/init.sh

and then issued

  coot

and it works.

If you don't source /sw/bin/init.sh, it won't work, and many other  
things in fink will be broken.  That is the only thing I can think  
of. Sorry if that isn't relevant.


Are you on 10.4?  I don't have access to 10.4 at the moment to test  
it...


Bill







On Feb 5, 2009, at 7:50 PM, Engin Ozkan wrote:


Hi everyone,

I still seem to have issues with fink'ed coot (revision-1847-1).  
It does not start and it gives an error

PYTHONPATH: Undefined variable.

I guess I could just define the PYTHONPATH, but I do not have a  
reason to. More interestingly, if I switch to zsh shell, I don't  
get the error and coot starts, even though I still don't have the  
variable defined.


Am I missing something here?

Thanks,

Engin

William Scott wrote:

Howdie Fulica aficionados:

coot-0.6-pre-1-revision-1847-1, available via fink (and my  
servers as binaries for 10.5), should be working properly now  
with python2.5.  It should also inherit $PYTHONPATH from your  
environment if you have set that (there is generally no need to,  
but you may have a reason).


HTH,

Bill

Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1

[William G. Scott]

On Feb 5, 2009, at 8:42 PM, Engin Ozkan wrote:


P.S. I am starting to like zsh more and more.



Me too.  zsh is the most fun I have ever had with my clothes on,  
except possibly when riding the new mountain bike.


zsh is to unix shells what OS X is to operating systems.  Programmable  
completions, including remote filename completion with scp alone make  
it worthwhile.


I started a zsh on OS X project, if anyone is interested:

http://code.google.com/p/zsh-templates-osx/

Re: [COOT] OS X: coot-0.6-pre-1-revision-1847-1

[William G. Scott]

OK, I just added the new fink info file to fink cvs for rev 1851.  I  
haven't had a chance to build it myself yet because I have to take my  
kids to school (such as it is in California).  I'll take the bad ones  
off the pre-built coot wiki page.



On Feb 6, 2009, at 7:16 AM, Engin Ozkan wrote:

Thanks, I knew things would be fixed by the time I woke up. I should  
have gone to bed earlier :)


Engin

Paul Emsley wrote:

Felix Frolow wrote:
I observe the same future in the recently installed (in the last  
hour) COOT (via FINK)


Dear Felix and Engin,

Thanks for your feedback - the source code for new version (1851)  
is available - more fun for Bill when he wakes up :)


Paul.

And on a slightly different note, this version also contains the  
following changed (improved?) dialog:


http://www.biop.ox.ac.uk/emsley/pictures/various/Screenshot-find-waters-dialog.png

Re: [COOT] coot0.6-pre-1 on FC10

[William G. Scott]

What happens if you turn off all compositing effects?


On Feb 23, 2009, at 8:37 AM, David Schwefel wrote:


Dear Coot community,

I encountered some problems using Coot on fedora core 10. I  
installed the
binaries, and upon starting, the system crashed just in the moment  
when the
Coot window appeared. I have a ATI radeon X1650 graphics card. When  
I switch
from the standard radeon to the ATI fglrx graphics driver, the  
system does

not crash anymore, but Coot quits with the following error message:

The program 'coot-real' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadRequest (invalid request code or no such  
operation)'.

 (Details: serial 661 error_code 1 request_code 143 minor_code 19)
 (Note to programmers: normally, X errors are reported asynchronously;
  that is, you will receive the error a while after causing it.
  To debug your program, run it with the --sync command line
  option to change this behavior. You can then get a meaningful
  backtrace from your debugger if you break on the gdk_x_error()  
function.)
coot-exe: "/usr/local/bin/coot-Linux-i386-fedora-10-gtk2-python/bin/ 
coot-real"

coot-version:
/usr/local/bin/coot-Linux-i386-fedora-10-gtk2-python/bin/coot-real
platform:
/bin/uname
core: #f
No core file found.  No debugging

Any hints how to solve this problem?

Best regards and thanks in advance,
David

Re: [COOT] python or scheme

[William G. Scott]

As far as learning scheme,



My $0.02:

From a purely practical standpoint, if, like me, you have limited  
time, energy and mental capacity, python would probably yield a better  
investment payback. There are numerous extensions available that make  
parsing things like pdb files very simple, there is the whole phenix/ 
cctbx resource you can make use of, and it is probably the most  
powerful and commonly employed scripting language among scientists  
(bioinformatics people like perl, for its text processing abilities).  
The syntax is very clean and straightforward and you don't have to  
deal with huge piles of dollar signs and parentheses all over the place.


Whichever you use, be sure to use an editor that employs an  
intelligent syntax highlighting mechanism, like vim, or even emacs (if  
you type with a lisp).  On OS X, TextMate is my editor of choice.


Here's  a site that lists some of the available modules:  
http://wiki.python.org/moin/NumericAndScientific

HTH,

Bill

Re: [COOT] [ccp4bb] coot crashes

[William G. Scott]

On Mar 2, 2009, at 4:25 AM, Vellieux Frederic wrote:


Any idea?


Is it there?

http://www.mail-archive.com/ubuntu-b...@lists.ubuntu.com/msg663049.html

Re: [COOT] Bring all windows to front?

[William G. Scott]

Yo Miguel:

I wrote a little helper zsh function/shell script called xtwit.

http://zsh-templates-osx.googlecode.com/svn-history/r53/trunk/Library/init/zsh/local-functions/darwin/xtwit


It wraps the command xwit (available via fink, for example) and gives  
you a gui that allows you to select a window to pop to the foreground:


<>



My guess is xwit itself could be tailored to do exactly as you want,  
and called from a python or scheme script.


eg:

xwit version 3.4

usage: xwit -display  -sync
-pop -iconify -unmap
-resize w h -rows r -columns c -[r]move x y
-[r]warp x y -colormap  -[no]save
-name  -iconname 
-bitmap  -mask  -[r]iconmove x y
-[no]backingstore -[no]saveunder
-[no]keyrepeat keycode ... keycode - keycode
-id  -root -current -select
-names ... [must be last]

HTH,

Bill



On Mar 5, 2009, at 8:30 AM, Miguel Ortiz Lombardia wrote:


Dear all,

I have looked in the manuals but haven't found anything concerning  
the possibility of bringing all coot windows to foreground. In Mac  
versions there is an annoying feature/bug consisting in some windows  
going behind the main graphic windows and being invisible in Apple's  
"Exposé", unless you happen to move your mouse over where they  
actually are. The ghost windows I call them. In this context, a  
"Bring all windows to front" or something similar would be helpful.  
If it would exist it would instantly become a button in my Menu bar...


BTW, has anyone else noticed that "Sort by Date" is not working?  
(again, in Mack fink coot)


Best,


Miguel
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2


--
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [COOT] Problem with coot

[William G. Scott]

; There are 2 data in
> /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CR.cif
> There are 2 data in
> /usr/local/xtal/coot/share/coot/lib/data/monomers/c/CD.cif
> There are 2 data in
> /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GR.cif
> There are 2 data in
> /usr/local/xtal/coot/share/coot/lib/data/monomers/g/GD.cif
> There are 2 data in
> /usr/local/xtal/coot/share/coot/lib/data/monomers/t/TD.cif
> There are 2 data in
> /usr/local/xtal/coot/share/coot/lib/data/monomers/u/UR.cif
> Reading coordinate file:
> /usr/local/xtal/coot/share/coot/standard-residues.pdb
>  PDB file /usr/local/xtal/coot/share/coot/standard-residues.pdb has been
> read.
> Spacegroup: P 1
> Cell: 40 109 93 90 90 90
>
> (coot-real:70225): Pango-WARNING **: Error loading GDEF table 0x6ead
>
> (coot-real:70225): Pango-WARNING **: Error loading GSUB table 0x6ead
>
> (coot-real:70225): Pango-WARNING **: Error loading GPOS table 0x6ead
> initalize graphics molecules...done.
> (filter-fileselection-filenames-state)
> (get-active-map-drag-flag)
> (use-graphics-interface-state)
> DEBUG:: stating pydirectory /usr/local/xtal/coot/share/coot/python
> INFO:: loading coot.py from /usr/local/xtal/coot/share/coot/python/coot.py
> Running python script /usr/local/xtal/coot/share/coot/python/coot.py
> INFO:: coot.py loaded
> INFO loading coot python modules
> Running python script
> /usr/local/xtal/coot/share/coot/python/coot_load_modules.py
> Loading: coot_utils.py
> Loading: filter.py
> Loading: coot_lsq.py
> Loading: shelx.py
> Loading: get_ebi.py
> Loading: local_code.py
> Loading: hello.py
> Good Afternoon Robertfloor, Welcome to Coot.
> (set-display-intro-string "Good Afternoon Robertfloor, Welcome to Coot.")
> Loading: mutate.py
> Loading: refmac.py
> Loading: libcheck.py
> Loading: gap.py
> Loading: fitting.py
> Loading: raster3d.py
> Loading: povray.py
> Loading: generic_objects.py
> Loading: ncs.py
> Loading: cns2coot.py
> Loading: tips.py
> Loading: americanisms.py
> Loading: group_settings.py
> Loading: brute_lsqman.py
> (filter-fileselection-filenames-state)
> (get-active-map-drag-flag)
> (use-graphics-interface-state)
> Loading scheme files from /usr/local/xtal/coot/share/coot/scheme
> load "filter.scm"
> load "matrices.scm"
> load "coot-utils.scm"
> load "coot-gui.scm"
> Coot Scheme Scripting GUI code found and loaded.
> load "coot-lsq.scm"
> load "shelx.scm"
> load "get-ebi.scm"
> WARNING: (net http client): imported module (net http message) overrides
> core binding `version'
> load "local-code.scm"
> load "hello.scm"
> Good afternoon Robert Floor. Welcome to Coot.
> (set-display-intro-string "Good afternoon Robert. Welcome to Coot")
> load "mutate.scm"
> load "refmac.scm"
> load "brute-lsqman.scm"
> load "libcheck.scm"
> load "gap.scm"
> load "fitting.scm"
> load "raster3d.scm"
> load "povray.scm"
> load "remote-control.scm"
> load "generic-objects.scm"
> load "fascinating-things.scm"
> load "ncs.scm"
> load "cns2coot.scm"
> load "clear-backup.scm"
> load "tips.scm"
> load "americanisms.scm"
> load "group-settings.scm"
> (set-display-lists-for-maps0)
> load "tips-gui.scm"
> load "extensions.scm"
> (filter-fileselection-filenames-state)
> (get-active-map-drag-flag)
> Loading ~/.coot...(set-add-terminal-residue-do-post-refine 1)
> done.
> (use-graphics-interface-state)
> (coot-checked-exit0)
> (clear-backups-maybe)
> There are 0 old files  (0 bytes) (0.0Mb) in "coot-backup"
> (stereo-mode-state)
> State file 0-coot.state.scm written.
> (save-state)
> State file 0-coot-history.py written.
> State file 0-coot-history.scm written.
>
> Some deprecated features have been used.  Set the environment
> variable GUILE_WARN_DEPRECATED to "detailed" and rerun the
> program to get more information.  Set it to "no" to suppress
> this message.
>
>


-- 
-


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

Please reply to:  wgsc...@chemistry.ucsc.edu

Re: [COOT] Problem with coot

[William G. Scott]

On Mar 28, 2009, at 10:14 AM, Robert wrote:


Recently I updated to coot-0.6-pre-1-1876 using fink
apparently something went wrong



robertfloor% /usr/local/xtal/coot/bin/coot


That is likely the origin of the problem, as this doesn't call fink's  
coot, but rather the one I made as a stand-alone.


Try this:

source /sw/bin/init.sh

coot

[COOT] coot-0.6-pre1-1941 for intel OS X 10.4/10.5

[William G. Scott]

This I hope will address previous grievances:

http://tinyurl.com/coot1941

Re: [COOT] coot-0.6-pre1-1941 for intel OS X 10.4/10.5

[William G. Scott]

On Mar 29, 2009, at 2:34 AM, Phil Evans wrote:


On 29 Mar 2009, at 04:42, William G. Scott wrote:


This I hope will address previous grievances:

http://tinyurl.com/coot1941


... except I get a load of errors I didn't have before :-(

and no splash screen or icons. The files all seem to be there. Any  
ideas?


I need to find a different line of employment.

This one apparently cured the same problem for Ralf that was occurring  
previously for him.



Just to humo(u)r me and perhaps enable diagnosis of the problem once  
and for all, what version of OS X, X11, and make of computer are you  
using?


Sorry for this.

Bill

Re: [COOT] Problem with standalone coot

[William G. Scott]

On Apr 3, 2009, at 3:08 AM, Simon Kolstoe wrote:


Thanks Bill,

I figured you meant:

source /usr/local/xtal/coot/bin/init.sh

which worked beautifully - my old sushi-eating coot has been  
replaced with a thoroughly more respectable picture!


Simon



I did, or for lobotoshell users,


source /usr/local/xtal/coot/bin/init.csh



The weird thing is that I had placed that very command as the first  
line of the coot wrapper shell script, so I thought that should be  
adequate.


Thanks.

Bill

Re: [COOT] DNA mutation

[William G. Scott]

Looks like you might be mutating into RNA (hence the non-canonical  
little r). But that is ok.  RNA is inherently more interesting.


On Apr 7, 2009, at 10:48 AM, Pierre Aller wrote:


Hi all,

I am using the last version of coot on mac OS X. I tried to mutate  
some nucleic acids and I encounter some problems.

It works fine for everything except for a mutation toward a Thymine.
I got this error message:
This should never happen - badness in get_standard_residue_instance,  
we selected 0 residues looking for residues of type :Tr: Oops -  
can't find standard residue for type Tr


Is it a bug, or am I doing something wrong?

Thanks,

Pierre



Pierre Aller Ph.D.
Postdoctorate Associate
University of Vermont   
201 Stafford Hall
95 Carrigan drive
Burlington, VT 05405-0084

Phone: 802-656-9534
mailto:pierre.al...@uvm.edu

Re: [COOT] coot dependency on $LANG?

[William G. Scott]

Could you (or we) set

LANG="en_US.US-ASCII"

in the coot wrapper script?


On Apr 29, 2009, at 8:01 AM, Steffen Schmidt wrote:


Hi,

I experienced a weird error (amino acids are not connected) when  
setting the environmental variable LANG to de_DE.UTF-8 (on a OS X  
10.5 machine). I guess this language setting is screwing up the PDB  
file parsing since german uses ',' as decimal separator…


BW
 Steffen

Re: [COOT] RSR exploding RNA

[William G. Scott]

On May 5, 2009, at 3:16 PM, CK wrote:


Hi all,
	I am refining a structure that contains RNA.  I've added hydrogens  
in the riding positions to help with maintaining proper geometry  
during refinement.  However, when I go to adjust the model between  
refinements in coot using Real Space Refine (or even Regularize for  
that matter) the RNA "explodes" with atoms going every which way.   
This didn't happen before I had added in hydrogens (with Molprobity  
via Reduce).  Also, when I Real Space Refine residues from the  
protein portion, the heavy atoms (C, O, N) behave normally while  
about half of the riding hydrogens go wandering off.  Any particular  
reason why this might be happening?



Hydrogen can be quite explosive.  Have you tried helium?

But seriously, if the program you used to hydrogenate uses a  
nomenclature that coot/refmac doesn't expect, this could happen.  Also  
the zero occupancy might be the culprit.


However you mentioned that without hydrogens it was hard to maintain  
proper geometry.  This might be a cause for concern, or re-examination  
of the structure and its density.

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

[William G. Scott]

I have the following guile-like stuff installed, if it is of any help:

diablo-% which dpkg-list
dpkg-list () {
dpkg --list \...@\*
}
diablo-% dpkg-list guile | grep "ii"
ii  guile-1.6-libs  
1.6.8-6.3ubuntu1 Main Guile libraries
ii  guile-1.8   
1.8.5+1-4.1ubuntu1   The GNU extension language  
and Scheme interp
ii  guile-1.8-dev   
1.8.5+1-4.1ubuntu1   Development files for Guile 1.8
ii  guile-1.8-doc   
1.8.5+1-4.1ubuntu1   Documentation for Guile 1.8
ii  guile-1.8-libs  
1.8.5+1-4.1ubuntu1   Main Guile libraries
ii  guile-g-wrap
1.9.11-1.1build1 scripting interface generator  
for C - Guile
ii  guile-gnome0-canvas 
2.15.95-2ubuntu1 Guile bindings for  
libgnomecanvas
ii  guile-gnome0-glib   
2.15.95-2ubuntu1 Guile bindings for GLib
ii  guile-goosh 
1.3-1Installs goosh
ii  guile-gui   
0.2-2Installs guile-gui for  
guile-1.8
ii  guile-lib   
0.1.6Installs guile-lib
ii  guile-net-http  
0.3.1-1  Installs the net-http scm file
ii  guile18-gtk 
2.0  guile-gtk-2.0 for guile18
ii  libguile-ltdl-1 
1.6.8-6.3ubuntu1 Guile's patched version of  
libtool's libltdl


I've also noticed that sometimes what the configure error reports  
isn't accurate when you look at the log files -- it might be choking  
on something else.


On May 12, 2009, at 8:11 AM, hari jayaram wrote:


Hello ,
The jaunty 32 bit build seems to fail ( with subversion revision  
2002 as

well)
It seems like based on what Ed Pozharsky wrote in ..its a problem  
with guile

in Ubuntu jaunty (9.04) ..

On my 32 bit , 9.04 installation , the build-it-gtk2-simple script  
chugs

along fine and then declares the following contradictory message

checking for Clipper... yes
Congratulations, you are using Guile
checking for guile... no
configure: error: guile required but not found

Regardless ..I will try Bill Scots or the CCP4 wiki
methodof

separately compiling all the coot dependencies . But though I would
wrote
in to inquire if there was already a simpler fix.

Thanks

Hari


On Fri, May 8, 2009 at 7:35 PM, Paul Emsley >wrote:



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.

Re: [COOT] problem with install on new Macbook Pro (OS X 10.5)

[William G. Scott]

Hi Jason:

For some reason that I don't understand, some users find they need to  
issue the command


source /usr/local/xtal/coot/bin/init.sh

prior to issuing the command

coot


("coot" in this context actually invokes a wrapper shell script that  
has that first source command in it, so that is why I don't understand  
why it isn't working.  If someone who is experiencing this problem  
feels like trying an experiment, just edit that shell script file /usr/ 
local/xtal/coot/bin/coot  and after the source line, add a line like


sleep 5

before the line that invokes coot-real. I can't reproduce the problem,  
so I can't test this.)


Sorry for the inconvenience.

Bill




On Jun 5, 2009, at 7:56 AM, Jason Greenwald wrote:


When I migrated to my new Macbook, COOT quit working properly.  The
icons/images do not appear for the majority of the GUI.  I tried all  
three
of the standalone binaries on Bill Scott's website.  The only thing  
that
works is the COOT app package from the CCP4 download site.  However  
with the
app package, I cannot have saved coot states for each directory that  
I work in.


This same problem has been previously reported several times on this  
mail

list but I could not find an answer.

Lrge list of errors on startup and they start with:

** (coot-real:2205): WARNING **: Error loading pixmap file:
/usr/local/xtal/coot/share/coot/pixmaps/display-manager.png
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/add-alt-conf.svg'
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/add-peptide-1.svg'
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/add-water.svg'
Error loading icon: Couldn't recognize the image file format for file
'/usr/local/xtal/coot/share/coot/pixmaps/anchor.svg'


Any ideas?
Thanks in advance,
Jason

[COOT] Coot with stereo LCD on OS X

[William G. Scott]

Yo people:

Following Warren DeLano's recommendations at pymol.org/zalman, I got a  
Zalman monitor for about $US 300, which, in California dollars, is  
about a week's worth of groceries at our local rat-infested Safeway.


The latest PyMOL and Coot both work great in stereo. I would go so far  
as to say these look as good as they did on my ca. $12K (1999 dollars)  
SGI R1s with Sony trinatron monitors, which I finally got rid of  
earlier this year. Also, the quality of the migraine these induce  
seems to be a bit more tolerable.


I found it worked fine with a Mac mini (the one my kids have connected  
to a TV to watch old Flintstones episodes), and also my wife's first  
generation iBook, the latter of which has no separate graphics card.  
So if you set it up with a mini, you can have a dedicated  
stereographics workstation with a reasonable quality monitor for under  
$1K (or just have a monitor and have your users bring their own laptop  
and a DVI connector.


It comes with DVI and VGA cables, and 1 pair of normal and one pair of  
clip-on circularly polarized glasses, and enough styrofoam packing to  
get rid of the last remaining wisps of an evanescent ozone layer.


Thanks to Paul (and Warren) for implementing this.

Bill


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

[COOT] Stereo Coot

[William G. Scott]

Dear Bernhard:

Thanks very much for implementing Zalman stereo into coot.  I  
apologize for neglecting to say so in my earlier email, and after  
previous cootbb emails, I have no excuse (except maybe fatigue).   
Thanks also for pythonizing coot, by the way, too.


All the best,

Bill

Re: [COOT] Coot with stereo LCD on OS X

[William G. Scott]

On Jul 29, 2009, at 3:34 AM, Paul Emsley wrote:


For me, the reference stereo image is Frodo on a E&S PS390.


I'm old(e) enough to remember having used that.



You might like to tweak the eye angle:

set_hardware_stereo_angle_factor(1.45) # or some such

(I am presuming that you are using the pythonic version).


The mac (fink) versions that we packaged use both python and scheme  
simultaneously at the same time all at once concurrently and in unison.







Thanks to Paul (and Warren) for implementing this.



For stereo support of Zalman M220W in Coot, credit should entirely  
go to Bernhard Lohkamp.


Sorry, I fscked up.  I have no excuse, given previous email exchanges,  
except to plead sleep deprivation and juvenile onset senility (but I  
remember the PS300).




Regards,

Paul.


Tootle pip.

Bill

Re: [COOT] Coot with stereo LCD on OS X

[William G. Scott]

Just for you (well, also me and anyone who wants it):

http://code.google.com/p/zsh-templates-osx/source/detail?r=138

(Powermate and Zalman monitor specific)


On Jul 30, 2009, at 6:30 PM, Wataru Kagawa wrote:


Hi Bill:

I am excited to hear that Coot works in stereo using the combination  
of the Zalman LCD display and Mac mini/iBook.

Is it possible to the same thing with a Mac Pro or an iMac (Intel)?

Thanks.

Wataru Kagawa

On 2009/07/29, at 16:08, William G. Scott wrote:


Yo people:

Following Warren DeLano's recommendations at pymol.org/zalman, I  
got a Zalman monitor for about $US 300, which, in California  
dollars, is about a week's worth of groceries at our local rat- 
infested Safeway.


The latest PyMOL and Coot both work great in stereo. I would go so  
far as to say these look as good as they did on my ca. $12K (1999  
dollars) SGI R1s with Sony trinatron monitors, which I finally  
got rid of earlier this year. Also, the quality of the migraine  
these induce seems to be a bit more tolerable.


I found it worked fine with a Mac mini (the one my kids have  
connected to a TV to watch old Flintstones episodes), and also my  
wife's first generation iBook, the latter of which has no separate  
graphics card. So if you set it up with a mini, you can have a  
dedicated stereographics workstation with a reasonable quality  
monitor for under $1K (or just have a monitor and have your users  
bring their own laptop and a DVI connector.


It comes with DVI and VGA cables, and 1 pair of normal and one pair  
of clip-on circularly polarized glasses, and enough styrofoam  
packing to get rid of the last remaining wisps of an evanescent  
ozone layer.


Thanks to Paul (and Warren) for implementing this.

Bill


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

Re: [COOT] Zalman & Coot

[William G. Scott]

Dear Jürgen:

I've been using the DVI cable provided and full resolution (I had to  
set this manually in display preferences).  I assume what works with  
my mini and my airbook would also work with a macbook pro.  I haven't  
tried the VGA option, but assume that would work too.


One thing I discovered is it doesn't work if you have display  
mirroring on.  If that is the case, turn it off in display  
preferences, and hopefully it will then work.


If not, try tilting the screen up or down a little bit (or move your  
head relative to the screen).


I went through a bit of frustration but it was all due to user error  
on my part.


Is the DVI cable just dead?

Did you issue the command in coot to start the stereo specific to  
Zalman mode?


Try the latest PyMOL too.  You have to rename it MacPyMOLZalman.app  
first.  Then open it, and if it isn't already in stereo, just hit the  
"stereo" menu item.


Depending on the positioning of the window, and number of pixels, you  
can have the image reversed, so check to see if that is happening, as  
it ruins the 3D effect.


Good luck.  Hope it is working for you soon.

Bill


On Aug 5, 2009, at 11:46 AM, Jürgen Bosch wrote:


Hi Bill,

I have received my two Zalmans yesterday and I wanted to try them  
out today. I don't seem to have the right settings I assume as I get  
a double vision image e.g. a loop that is supposed to be in the back  
in 3d splits up and you can see two lines (that's as Calpha). I have  
played with the resolution of the monitor to decrease it to 768x1024  
but the two lines still persist.
I'm using the latest  15" MacBookPro via MiniDisplayport to VGA as  
the DVI does not seem to work with the cable provided by Zalman I  
assume.


My coot is
0.6-pre-1 rev 2037

I turned of spaces and enabled mirroring to keep it simple but I'm  
not quite happy right now. I have not yet tried Pymol as my version  
does not support the Zalman monitors.


Any suggestions what I can try to get rid of the double lines ?

Thanks,

Jürgen

-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://web.me.com/bosch_lab/

Re: [COOT] MacOS and Zalman

[William G. Scott]

On Aug 19, 2009, at 1:14 AM, Lutz Schmitt wrote:


Dear Bill,

I am probably one of the many people out here who asked you a  
question concerning the Zalman 3D monitor.


We got one yesterday and I upgraded coot to coot 0.6-pre-1 (revision  
2215) running on a Quad-Core Intel with a NVidia Qudro FX 5600 (=S  
10.5.7). I use the DVI cable, mirroring off and the Zalman is the  
"second" monitor.


Running coot at the highest resolution 1680x1050 and 60 Hz (more is  
not possible according to the monitor settings) I have the feeling  
that I close but not really there. In coot, I can see two images,  
the 3D effect is there but not perfect yet and without the polarize  
glasses the screen flickers. However, the situation reminds me of  
using Crystal eyes and a refresh rate, which is too small meaning I  
am almost there.


I think you can increase the stereo angle.  I need to appeal to Paul  
or Bernhard for the appropriate command (hence the cc to the cootbb).


Does it work ok with pymol?




Do you know what I am doing wrong?


No.  Quite possibly nothing.  It is also possible you are seeing the  
exact same thing as I am, but because of my small brain and limited  
cranial capacity, I get a different visual effect.


BTW, I still use bash not zsh. Therefore I have not used your  
scripts yet.


You can run any shell script (including zsh functions) by making it  
executable and run it in the usual way from one of the other shells.




Many thanks in advance

Lutz

Re: [COOT] MacOS and Zalman

[William G. Scott]

On Aug 19, 2009, at 8:21 AM, Paul Fyfe wrote:


  (set-hardware-stereo-angle-factor 1.3)



This is I think the command I was after.

Thanks.

Re: [COOT] MacOS and Zalman

[William G. Scott]

Hi Lutz:

Yeah, that is definitely the problem.  That kind of "hardware stereo"  
is for a CRT and the special video card it needs.


Fortunately, we don't need any of that.

Try issuing the scheme command

(zalman-stereo-mode)

AFAIK, it is not yet implemented as a menu item (but you can make one,  
which is what I did).


I am also using the DVI cable and adaptor, fwiw.

Bill


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott



On Aug 19, 2009, at 11:36 AM, Lutz Schmitt wrote:


Hi Bill,

yes I have a first-generation airbook as well. I started coot, moved  
the coot window to the Zalman monitor and used , ,  
 to activate it, but as I said coot "told" me that  
stereo was not possible. Should I start to force coot to start on  
the Zalman? If so, do I have to "make" the Zalman the primary screen?


Cheers

Lutz

Am 19.08.2009 um 19:01 schrieb William Scott:


Hi Lutz:

Yes, mine is working with a first-generation airbook.  I didn't do  
anything special.  How are you activating stereo on coot (what  
command)?


Bill


William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/




On Aug 19, 2009, at 9:59 AM, Lutz Schmitt wrote:


Dear Bill,

many thanks!

Well with pymol the same - near there but only nearly.

I did two more thing so far. Installed the newest coot release on  
my airbook and simply connected the Zalman (VGA connector). Here,  
coot tells me that stereo can not be enabled  and nothing  
happend. According to your email to Jürgen, you got it to work on  
your Airbook. Or am I missing something?


Furthermore, I checked the quadro compatibility list of Zalman -  
it ends with the FX 5500, the 5600 is not included. Is that a  
possible explanation. We have another Mac with the FX 4500  
installed. According to the list it should be supported (at least  
on XP).


But most of all - I am really interested to learn about the stereo  
angle :-)


Cheers

    Lutz

Am 19.08.2009 um 16:36 schrieb William G. Scott:



On Aug 19, 2009, at 1:14 AM, Lutz Schmitt wrote:


Dear Bill,

I am probably one of the many people out here who asked you a  
question concerning the Zalman 3D monitor.


We got one yesterday and I upgraded coot to coot 0.6-pre-1  
(revision 2215) running on a Quad-Core Intel with a NVidia Qudro  
FX 5600 (=S 10.5.7). I use the DVI cable, mirroring off and the  
Zalman is the "second" monitor.


Running coot at the highest resolution 1680x1050 and 60 Hz (more  
is not possible according to the monitor settings) I have the  
feeling that I close but not really there. In coot, I can see  
two images, the 3D effect is there but not perfect yet and  
without the polarize glasses the screen flickers. However, the  
situation reminds me of using Crystal eyes and a refresh rate,  
which is too small meaning I am almost there.


I think you can increase the stereo angle.  I need to appeal to  
Paul or Bernhard for the appropriate command (hence the cc to the  
cootbb).


Does it work ok with pymol?




Do you know what I am doing wrong?


No.  Quite possibly nothing.  It is also possible you are seeing  
the exact same thing as I am, but because of my small brain and  
limited cranial capacity, I get a different visual effect.


BTW, I still use bash not zsh. Therefore I have not used your  
scripts yet.


You can run any shell script (including zsh functions) by making  
it executable and run it in the usual way from one of the other  
shells.




Many thanks in advance

Lutz

Re: [COOT] MacOS and Zalman

[William G. Scott]

Hi Lutz:


On Aug 19, 2009, at 11:59 AM, Lutz Schmitt wrote:


Hi Bill,

thanks! But now comes the ignorant part from my site :-)

As a non-native speaker, I do understand AFAIK (as far as I know?),  
but what do you mean by fwiw? - sorry


Hence the "wtf" utility:

% fink list wtf
Information about 9261 packages read in 3 seconds.
 i   wtf  20080626-1 Translates common  
Internet acronyms


% wtf fwiw
FWIW: for what it's worth

% wtf afaik
AFAIK: as far as I know


% wtf wtf
WTF: {what,when,where,who,why} the f---




Furthermore, I use coot and Macs and I appreciated more than once  
all your input. Since you did such a wonderful job, I have never  
bothered much with fiddling around with coot. I just took what you  
developed. Therefore, I have to ask the stupid and ignorant  
question: how do I issue a scheme??


You can issue commands in either the scheme scripting language or the  
python scripting language.


To issue a scheme command, just do the following:

1.  Start coot and go to the "Calculate" menu item.

2.  In the pull-down, the second-to-last entry is "Scripting ...".  Go  
to that and select the "Scheme" option.


3.  Paste in the command (zalman-stereo-mode) including the  
parentheses into the top window where it says "Command:"


4.  Hit the return key and you should now be getting a double image.



In other words, could you please direct me to your scheme or send it  
to me? I hope that the fact that I still stick to bash and have not  
changed to zsh makes no problem. Again, blame my ignorance!


Don't worry, it has nothing to do with what shell you choose.  It will  
work the same whether you use bash/zsh/tcsh.




Sorry for my ignorance


Never apologize for asking questions.  If you do a mail search, you  
will see that I am the ignorance king.


But if you are feeling adventurous, right-click on the second line of  
the menu bar in the blank area next to where it says "Display  
Manager".  Select "Add a user-defined button"  and make yourself a  
Zalman Stereo button, and then feel smug about what a power user you  
now are.


I think you will need the python version of the command, instead of  
the scheme version, which is  zalman_stereo_mode()


Note the underscores and different placement of the parentheses.

There is even an appropriate icon in row five, column eight, you can  
select when prompted for an icon.





Lutz

Am 19.08.2009 um 20:41 schrieb William G. Scott:


Hi Lutz:

Yeah, that is definitely the problem.  That kind of "hardware  
stereo" is for a CRT and the special video card it needs.


Fortunately, we don't need any of that.

Try issuing the scheme command

(zalman-stereo-mode)

AFAIK, it is not yet implemented as a menu item (but you can make  
one, which is what I did).


I am also using the DVI cable and adaptor, fwiw.

Bill


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott



On Aug 19, 2009, at 11:36 AM, Lutz Schmitt wrote:


Hi Bill,

yes I have a first-generation airbook as well. I started coot,  
moved the coot window to the Zalman monitor and used ,  
,  to activate it, but as I said coot  
"told" me that stereo was not possible. Should I start to force  
coot to start on the Zalman? If so, do I have to "make" the Zalman  
the primary screen?


Cheers

Lutz

Am 19.08.2009 um 19:01 schrieb William Scott:


Hi Lutz:

Yes, mine is working with a first-generation airbook.  I didn't  
do anything special.  How are you activating stereo on coot (what  
command)?


Bill


William G. Scott

Contact info:
http://chemistry.ucsc.edu/~wgscott/




On Aug 19, 2009, at 9:59 AM, Lutz Schmitt wrote:


Dear Bill,

many thanks!

Well with pymol the same - near there but only nearly.

I did two more thing so far. Installed the newest coot release  
on my airbook and simply connected the Zalman (VGA connector).  
Here, coot tells me that stereo can not be enabled  and  
nothing happend. According to your email to Jürgen, you got it  
to work on your Airbook. Or am I missing something?


Furthermore, I checked the quadro compatibility list of Zalman -  
it ends with the FX 5500, the 5600 is not included. Is that a  
possible explanation. We have another Mac with the FX 4500  
installed. According to the list it should be supported (at  
least on XP).


But most of all - I am really interested to learn about the  
stereo angle :-)


Cheers

Lutz

Am 19.08.2009 um 16:36 schrieb William G. Scott:



On Aug 19, 2009, at 1:14 AM, Lutz Schmitt wrote:


Dear Bill,

I am probably one of the many people out here who asked you a  
question concerning the Zalman 3D monitor.


We got one yesterday and I upgraded coot to coot 0.6-pre-1  
(revision 2215) running on a Quad-Core Intel with a NVidia  
Qudro FX 5600 (=S 10.5.7). I use the DVI cable, mirroring off  
and the Zalman is the

[COOT] Need help with coot wiki

[William G. Scott]

I just started a stereographics section on the coot wiki, but need  
help, specifically with the hardware stereo part from someone with  
firsthand experience, but feel free to improve all of it:


http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Stereographic_Display

[COOT] Apple OS X 10.6, X11.app, and coot

[William G. Scott]

Hi Citizens:

If you have installed Apple's X11 v. 2.4.0, and "upgrade" to OS X 10.6  
(Snow Leopard), you will be displeased to discover X11 gets downgraded  
with no warning, and (unlike before), there is no mechanism to restore  
X11.


I recovered by copying the 2.4.0 version of  /usr/X11/lib/ 
libfontconfig.1.dylib into the "new" X11 /usr/lib directory.


You can grab it here if you have similar issues:

<http://sage.ucsc.edu/~wgscott/downloads/?C=M;O=D>

Bill

Begin forwarded message:


From: "William G. Scott" 
Date: August 28, 2009 4:52:34 PM PDT
To: Jeremy Huddleston 
Cc: x11-us...@lists.apple.com
Subject: Re: SL's X11 (X11-users Digest, Vol 6, Issue 177)

Hi Jeremy:

Thanks.

I just replaced the SL /usr/X11/lib/libfontconfig.1.dylib with the  
one I had from an X11-2.4.0 install on another computer and it  
solved at least this problem.


Fink used to give the users the option of installing its own X11,  
but I thought they got talked out of it by Apple for 10.5.


I guess I have a different idea of what "robust" is.

Bill


On Aug 28, 2009, at 4:44 PM, Jeremy Huddleston wrote:


On Aug 28, 2009, at 16:25, William G. Scott wrote:

I've compiled a bunch of stuff using 2.4.0 on 10.5.

I just upgraded to 10.6, which regressed X11 without warning, and  
there is no way out for the next four months except to recompile  
everything or wait until December?


You should recompile all your fink/MacPorts when you upgrade the OS  
anyways...


Yes, the X11 included with OSX 10.6 is 2.3.4.  It is newer /  
compatible with anything compiled against Leopard's X11 (2.1.6) or  
something compiled against 2.3.3.2 or earlier from macosforge.org.


MacPorts uses their own X11 packages rather than the system X11  
packages and is therefore (IMO) more robust than fink which uses  
the system X11... but that's another discussion entirely.



% /sw/bin/coot
dyld: Library not loaded: /usr/X11/lib/libfontconfig.1.dylib
Referenced from: /sw/bin/coot-real
Reason: Incompatible library version: coot-real requires version  
6.0.0 or later, but libfontconfig.1.dylib provides version 5.0.0


Please say it ain't so, or is there a way to force-install 2.4.0  
in 10.6?


No... and trying to do so will give you problems down the road.  As  
mentioned, 2.4.1 for SL will NOT install in /usr/X11 and will  
therefore be more robust to the SU process.

Re: [COOT] Apple OS X 10.6, X11.app, and coot

[William G. Scott]

On Aug 29, 2009, at 11:15 AM, Nayden Koon wrote:

I thought I'd try get away with 2.3.4 X11, when I had issues I  
thought maybe I needed 2.4, but noticed that doesn't even install on  
10.6.


I noticed that too, and had the temerity to ask:

http://lists.apple.com/archives/X11-users/2009/Aug/msg00135.html

Re: [COOT] Apple OS X 10.6, X11.app, and coot

[William G. Scott]

I just made a new stand-alone coot last night and verified it works on  
10.5 and 10.6 intel:


http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot

It was the last thing I did on sage before updating.

or, you can jump-start fink on 10.6 :

http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/64-bit_Fink_for_10.5_and_10.6



On Sep 2, 2009, at 8:45 AM, Abhinav Kumar wrote:


I don't recall. It was installed a long while ago.

Should I uninstall it and re-instal using fink?
Please give me some detailed instructions.

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 Sep 2, 2009, at 8:43 AM, William G. Scott wrote:



On Sep 2, 2009, at 8:40 AM, Abhinav Kumar wrote:

Reason: Incompatible library version: DictionaryServices  
requires version 10.0.0 or later, but libxml2.2.dylib provides  
version 9.0.0


This line says a different libxml2.2.dylib exists somewhere

Is this a CCP4 coot?

[COOT] 64-bit coot on OS X still buggy

[William G. Scott]

Hi folks:

It turns out the 64-bit coot on OS X 10.6 is a bit buggy.

32-bit seems ok.

If you need a recent 32-bit stand-alone for 10.5 or 10.6,  
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot

Real-space refinement and map fitting causes a crash that I will need  
some expert help fixing (how's it going, Paul?).


Sorry.

Bill


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

Re: [COOT] 64-bit coot on OS X still buggy

[William G. Scott]

I don't know if it is the newer version or changing gcc (back to) what  
Apple provides, but I think rev2265 fixes it (it did for me).


The superposition GUI still reliably crashes coot in 64-bit mode for  
some reason (independent of ssm vs lsq).



On Sep 4, 2009, at 9:28 AM, William G. Scott wrote:


Hi folks:

It turns out the 64-bit coot on OS X 10.6 is a bit buggy.

32-bit seems ok.

If you need a recent 32-bit stand-alone for 10.5 or 10.6,  
http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Stand-Alone_Coot

Real-space refinement and map fitting causes a crash that I will  
need some expert help fixing (how's it going, Paul?).


Sorry.

Bill


William G. Scott

contact info:  http://chemistry.ucsc.edu/~wgscott

Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11

[William G. Scott]

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 0.001 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

Re: [COOT] Coot osx 10.6 problem

[William G. Scott]

The "good" news is I can reproduce your error:

checking for GtkGLExt - version >= 1.0.0... no
*** Could not run GtkGLExt test program, checking why...
*** The test program failed to compile or link. See the file  
config.log for the
*** exact error that occured. This usually means GtkGLExt is  
incorrectly installed.

### execution of /var/tmp/tmp.2.JleDIx failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.6-pre-1-revision-2283-1
(Reading database ... 201033 files and directories currently installed.)


I'm coming to the conclusion that upgrading 32-bit fink to SL on a 64- 
bit capable machine is more trouble than a fresh install of 64-bit fink.


I'll try to get this sorted out.  Sorry.

Bill




On Sep 8, 2009, at 7:30 AM, Dima Chirgadze wrote:


Dear Bill,

I am having problems installing latest version of coot under snow  
leopard.


1) I have installed fink 0.29.9 (32-bit) via bootstrapping on a Snow  
Leopard machine.


2) changed the /sw/etc/fink.conf according to your website and  
updated fink


3) changed /sw/etc/apt/sources.list to include
deb  http://sage.ucsc.edu/fink_intel_10.6_32bit stable main crypto
deb  http://sage.ucsc.edu/fink_intel_10.6_32bit unstable main crypto
deb  http://sage.ucsc.edu/fink_intel_10.6_32bit local main

4) when I do: fink -b install coot, it installs/updates about 100  
packages and then I get the following error:

--snip--
checking for pkg-config... (cached) /sw/bin/pkg-config
checking for GtkGLExt - version >= 1.0.0... no
*** Could not run GtkGLExt test program, checking why...
*** The test program failed to compile or link. See the file  
config.log for the
*** exact error that occured. This usually means GtkGLExt is  
incorrectly installed.

### execution of /var/tmp/tmp.2.MhYZKK failed, exit code 1
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.6-pre-1-revision-2265-1
(Reading database ... 25946 files and directories currently  
installed.)

Removing fink-buildlock-coot-0.6-pre-1-revision-2265-1 ...
Failed: phase compiling: coot-0.6-pre-1-revision-2265-1 failed
--snip--

I've searched the lists but couldn't get it working

I tried re-installing gtkglext1 and gtkglext1-shlibs. The  
$LD_LIBRARY_PATH and/or $DYLD_LIBRARY_PATH both are unset. I still  
cannot install. Could you please help me to resolve it?


Thank you very much in advance,

Regards,

Dima


Dimitri (aka Dima) Chirgadze, PhD
Senior Research Associate
Department of Biochemistry
University of Cambridge
Cambridge, CB2 1GA
UK
Tel: +44 1223 766029
Fax: +44 1223 766082

Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11

[William G. Scott]

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 0.001 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

Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11

[William G. Scott]

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 0.001 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

[COOT] A general plea

[William G. Scott]

We could make life a lot more attractive than the alternatives for our  
beloved coot developers if we keep current with operating systems, so  
that they could focus on new features rather than backward- 
compatability that they can only test with the aid of time travel or  
frequent trips to the Smithsonian.


For OS X, the 10.6 upgrade for intel is incredibly stable, 64-bit, and  
US$30 (and doesn't require a previous OS, contrary to claims to the  
contrary).  For ppc, 10.5.8 is the final destination. (For anyone  
using stuff I compile, these two options are all I can do at the  
moment.)


For Linux, RH3 is older than my first-grader.  You can upgrade, or  
better yet, switch to Ubuntu, which is free and has great  
internationalization support. I did this five or six years ago and  
never looked back.


For Windows, I think 2000 might be stable now.

Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11

[William G. Scott]

On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote:


hink it's time to upgrade to 10.6, finally!


10.6.1  now.

:D

Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11

[William G. Scott]

Dear Christian:

I'm getting it now too.  I forgot to cc you.  I get it on 32-bit but  
not 64-bit SL.  I've sent the crash report to Paul .


Check to see if you have anything in

~/Library/Logs/DiagnosticReports

that has "coot" in the title and a recent date.

Bill



On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote:


Dear Bill,

Thanks for your quick reply!  I installed the new revision but it  
doesn't seem to make a difference (to my problems). I guess you're  
right and it's because I am still running 10.4 - think it's time to  
upgrade to 10.6, finally!


Again, many thanks and best regards,

Christian


Am 08.09.09 16:14 schrieb "William G. Scott" unter >:


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 0.001 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

Re: [COOT] buggy coot 0.6-pre-1 r2264 on OS X 10.4.11

[William G. Scott]

Paul just pulled off a heroic fix (rev 2310).  Please try that.




On Sep 11, 2009, at 7:40 AM, William G. Scott wrote:


Dear Christian:

I'm getting it now too.  I forgot to cc you.  I get it on 32-bit but  
not 64-bit SL.  I've sent the crash report to Paul .


Check to see if you have anything in

~/Library/Logs/DiagnosticReports

that has "coot" in the title and a recent date.

Bill



On Sep 11, 2009, at 7:36 AM, Benda, Christian wrote:


Dear Bill,

Thanks for your quick reply!  I installed the new revision but it  
doesn't seem to make a difference (to my problems). I guess you're  
right and it's because I am still running 10.4 - think it's time to  
upgrade to 10.6, finally!


Again, many thanks and best regards,

Christian


Am 08.09.09 16:14 schrieb "William G. Scott" unter >:


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 0.001 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

Re: [COOT] call for beta testers

[William G. Scott]

On Sep 14, 2009, at 3:23 PM, Paul Emsley wrote:


So the last couple of days have been a bit frustrating for me, but a
good deal of credit goes to Bill of course.



This can be read in at least two ways.


As anyone who knows me could tell you, the only thing I really can  
take credit for is constant, relentless complaining.

Re: [COOT] fink remove old packages

[William G. Scott]

Fink cleanup.

You can blow away all the debian. Packages if you don't compiler stuff

William G. Scott

(via iPod and gmail -- forgive the typos and brevity)

Please reply to wgsc...@chemistry.ucsc.edu

On Sep 15, 2009, at 8:32 AM, Andreas Förster   
wrote:



Hey all (especially Bill, I guess),

I was bushwhacking through the fink jungle on my MacBook Pro  
(10.5.8) today and realized just how vast it it.  There are 18GB in / 
sw.  As examples (and to make this email uncannily on-topic), there  
are 18 coot_0.6-pre-1-revision--?_darwin-i386.deb packages and  
14 coot_0.5-pre-1-*_darwin-i386.deb packages in /sw/fink/10.4/ 
unstable/main/binary-darwin-i386/sci.


Is this necessary?  How do I clean fink up?  I should say that I  
compile everything from source.


Thanks.


Andreas




--
   Andreas Förster, Research Associate
   Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
   http://www.msf.bio.ic.ac.uk

Re: [COOT] fink remove old packages

[William G. Scott]

Let's try this again:

fink cleanup

will remove all but the most current debian packages (these are  
essentially tar-like archives of the packages).


If you don't actually compile stuff on the laptop, but instead use my  
repositories, there really is no need to keep any of the debian  
package files.  For ccp4 and coot these can consume a lot of disk  
space.  You can remove all of them, and should you ever need one, you  
can always download it again.


Another thing you can do, following the installation of Xcode, is to  
remove the /Developer directory.  All the important compiler-type  
stuff gets installed into /usr/bin and so forth anyway.




On Sep 15, 2009, at 8:45 AM, William G. Scott wrote:


Fink cleanup.

You can blow away all the debian. Packages if you don't compiler stuff

William G. Scott

(via iPod and gmail -- forgive the typos and brevity)

Please reply to wgsc...@chemistry.ucsc.edu

On Sep 15, 2009, at 8:32 AM, Andreas Förster   
wrote:



Hey all (especially Bill, I guess),

I was bushwhacking through the fink jungle on my MacBook Pro  
(10.5.8) today and realized just how vast it it.  There are 18GB  
in /sw.  As examples (and to make this email uncannily on-topic),  
there are 18 coot_0.6-pre-1-revision--?_darwin-i386.deb  
packages and 14 coot_0.5-pre-1-*_darwin-i386.deb packages in /sw/ 
fink/10.4/unstable/main/binary-darwin-i386/sci.


Is this necessary?  How do I clean fink up?  I should say that I  
compile everything from source.


Thanks.


Andreas




--
  Andreas Förster, Research Associate
  Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
  http://www.msf.bio.ic.ac.uk

Re: [COOT] fink remove old packages

[William G. Scott]

After "fink cleanup", you can hfs-compress (only on 10.6) and gain  
another factor of two free space:


I tested this on my wife's laptop, just to be safe:

Before:
% du -h -d 1 /sw
300K/sw/Applications
  84M/sw/bin
3.1M/sw/etc
  61M/sw/fink
4.0M/sw/include
604M/sw/lib
112K/sw/Library
648K/sw/sbin
2.2G/sw/share
5.1M/sw/src
1.1G/sw/var
4.0G/sw


Then do:

sudo mv /sw  /sw.1
sudo ditto --hfsCompression  /sw.1  /sw
sudo rm -rf /sw.1


After:
% du -h -d 1 /sw
  64K/sw/Applications
  33M/sw/bin
508K/sw/etc
6.1M/sw/fink
484K/sw/include
199M/sw/lib
  44K/sw/Library
208K/sw/sbin
738M/sw/share
5.1M/sw/src
1.0G/sw/var
2.0G/sw

I think it might be faster, too, but I'm not certain.


This also works great with diffraction images.

Bill


On Sep 15, 2009, at 8:32 AM, Andreas Förster wrote:


Hey all (especially Bill, I guess),

I was bushwhacking through the fink jungle on my MacBook Pro  
(10.5.8) today and realized just how vast it it.  There are 18GB in / 
sw.  As examples (and to make this email uncannily on-topic), there  
are 18 coot_0.6-pre-1-revision--?_darwin-i386.deb packages and  
14 coot_0.5-pre-1-*_darwin-i386.deb packages in /sw/fink/10.4/ 
unstable/main/binary-darwin-i386/sci.


Is this necessary?  How do I clean fink up?  I should say that I  
compile everything from source.


Thanks.


Andreas




--
   Andreas Förster, Research Associate
   Paul Freemont & Xiaodong Zhang Labs
Department of Biochemistry, Imperial College London
   http://www.msf.bio.ic.ac.uk

[COOT] I wish I could lose weight like this (OS X 10.6)

[William G. Scott]

Hi Folks:

On OS X, 10.6, I have been playing around with hfsCompression.  I can  
decrease the size of /sw/share/coot significantly:


% cd /sw/share/
% du -h -d 0 coot
180Mcoot

% sudo mv coot coot.1
% sudo ditto --hfsCompress coot.1 coot
% du -h -d 0 coot
 31Mcoot

This can also be done with the libraries and binaries, and even the  
whole of /sw.


It squeezed phenix down to 319 MB from 1.1 GB.  CCP4's new footprint  
is 562 MB, instead of 1.5 GB.


hfscompressing Xray data results in a factor of two space-saving.

The files still look the same from the point of view of the operating  
system.  You can in fact only "see" the compression using commands  
like du or df.


More here:


Bill

Re: [COOT] problem updating coot using fink

[William G. Scott]

Dear Eleonore:

As you mentioned, everyone who upgraded 32-bit fink on 10.6 runs into  
this.  If you start fresh (either 32-bit or 64-bit), the problem  
doesn't arise.


I hope you don't mind me cc-ing the cootbb, as this problem is a  
general one.


The advice I was given, and with some reluctance, I followed, was to  
delete every *.la file in /sw.


The easiest way to do this is using the zsh shell:


sudo /bin/zsh
cd /sw/lib
/bin/rm -f **/*.la


The "**" is a zsh-shell specific wildcard for recursive globbing.

I had to rebuild a couple of other packages too, but unfortunately  
didn't keep notes.


64-bit coot and ccp4 are working great, by the way.

All the best,

Bill


On Sep 24, 2009, at 7:53 AM, Eleonore von Castelmur wrote:


Dear Bill

Sorry to disturb, but I have recently encountered the same problem  
as you did  when updating coot on OS X 10.6 as you did (coot-0.6- 
pre-1-revision-2334-1) when you wrote to the fink list:


libtool: link: cannot find the library `/usr/X11/lib/libXrender.la'
make[1]: *** [coot-tiddly] Error 1
make: *** [all-recursive] Error 1
### execution of /var/tmp/tmp.2.96Zqrl failed, exit code 2
Removing runtime build-lock...
Removing build-lock package...
/sw/bin/dpkg-lockwait -r fink-buildlock-coot-0.6-pre-1-revision-2334-1
(Reading database ... 82665 files and directories currently  
installed.)

Removing fink-buildlock-coot-0.6-pre-1-revision-2334-1 ...
Failed: phase compiling: coot-0.6-pre-1-revision-2334-1 failed

I have tried to update several times after running fink self-update  
as well as using fink -y install coot. I have found and read the   
corresponding answer you received that removing every .la file from  
the Fink tree does the job. I am unsure about how to proceed though.  
I would appreciate any tips.


Best,

Eleonore

PS: In case it is relevant, I followed the update procedure you  
posted to upgrade fink to 10.6.


°
Eleonore von Castelmur
School of Biological Sciences
Crown Street
Liverpool
L69 7ZB
Work +44 151 795 4498