Re: [COOT] Graphics problem running Coot with EdUbuntu 8.10

2009-05-11 Thread Stephen Graham
Hi Shaun,

Have you tried turning off compiz?
(System  Preferences  Appearance  Visual Effects: Select 'None')

Cheers,

Stephen

On 11/05/2009, Shaun Lott s.l...@auckland.ac.nz wrote:
 Hi

  Apologies if this problem has been dealt with elsewhere - I scanned the
  archives but couldn't see anything that looked similar.

  I'm about to use Coot as part of a graduate teaching exercise. Version 0.52
  starts ok, and can load co-ords and maps, but whenever one clicks, the
  screen gets corrupted - see attached image. You can get a normal view back
  by rotating the molecule, but the whole user experience is a pretty
  frustrating one, as it is pretty much impossible to click on anything. The
  fault seems to be hardware and Coot version independent - it manifests in
  0.5.2 and also using
  0.6-pre-1-revision-1997-binary-Linux-i686-ubuntu-8.04.2, though less
  dramatically in the latter - just a grey screen rather than the corrupted
  one. The same thing occurs when using a Dell or an iMac running Ubuntu
  (don't ask...)

  So I'm guessing it's a(n) Ubuntu thing. The machine are running the same
  versrion of EdUbuntu 8.10, details as below.

  Has anyone else seen this? Does anyone have a fix?

  cheers

  Shaun

   cat /proc/version
  Linux version 2.6.27-7-generic (bui...@palmer) (gcc version 4.3.2 (Ubuntu
  4.3.2-1ubuntu11) ) #1 SMP Tue Nov 4 19:33:20 UTC 2008





-- 
Dr Stephen Graham
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549


[COOT] Scheme on WinCoot (Win XP)

2009-05-11 Thread Alex Luso
Hi,

  I am new to Coot - I have been experimenting with the examples on the wiki
page and it appears that scheme/guile scripting does not work in WinCoot
(0.5.2). Just wanted to confirm if I am correct.

  I am/was a little confused b/c it appears the libraries and paths to
scheme/guile get installed but nothing happens if I try to run a scheme script.

  Also read the slightly cryptic message you can install an add-on for
scheme/guile scripting (no warranties) in
http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot.html
but I haven't seen this add-on anywhere.

  Just wanted to avoid re-writing some nice scheme scripts I see here and
there and to just get some information on the subject.

  Thanks!
  -Alex


Re: [COOT] Scheme on WinCoot (Win XP)

2009-05-11 Thread Bernhard Lohkamp
Hi,

ok to clarify the situation with respect to Scheme/guile in WinCoot:

In general it is possible to compile and run WinCoot with Scheme,
however we currently DO NOT distribute WinCoot with Scheme enabled (note
to self: change website). The reason for this is that no text can be
displayed in the Scheme (Gtk) widgets and I/we want to avoid endless
commenting on this. Maybe there should be some low level implementation
without the use of fancy (scheme) widgets, so that at least scripts can
be run.. (on my - long - list now).

B

  I am new to Coot - I have been experimenting with the examples on 
 the wiki
 page and it appears that scheme/guile scripting does not work in 
 WinCoot(0.5.2). Just wanted to confirm if I am correct.
 
  I am/was a little confused b/c it appears the libraries and paths to
 scheme/guile get installed but nothing happens if I try to run a 
 scheme script.
 
  Also read the slightly cryptic message you can install an add-on 
 forscheme/guile scripting (no warranties) in
 http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot.html
 but I haven't seen this add-on anywhere.
 
  Just wanted to avoid re-writing some nice scheme scripts I see 
 here and
 there and to just get some information on the subject.
 
  Thanks!
  -Alex
 



***

Dr. Bernhard Lohkamp
Assistant Professor
Div. Molecular Structural Biology
Dept. of Medical Biochemistry and Biophysics (MBB)
Karolinska Institutet
S-17177 Stockholm
Sweden

phone: (+46) 08-52487673
fax:   (+46) 08-327626
email: bernhard.lohk...@ki.se


[COOT] ELFCLASS64

2009-05-11 Thread Ed Pozharski
After recent upgrade to Ubuntu 9.04, coot binaries that worked fine
before started reporting the ELFCLASS64 error when loading a
particular library, namely /usr/lib/libguile-srfi-srfi-1-v-3.so.3.  

I understand that the real root of this problem is my bizarre obsession
with installing 64-bit Linux and then being too lazy to compile coot
from source and instead trying to use 32-bit coot binaries.  To resolve
the ELFCLASS64 issue, I downloaded guile1.8 32-bit debian package from
ubuntu repositories and placed libraries into /usr/lib32.  That, of
course, didn't help and I had to redirect the symbolic link in /usr/lib
to /usr/lib32.  Now coot runs fine, but this is an ugly fix, not to
mention that it may cost me down the road when some 64-bit application
discovers that I substituted the library.  At the same time, I see that
$COOT_PREFIX/lib contains all the libraries, and so my question is why
coot tries to load libraries from /usr/lib?  Should I uninstall guile
via synaptic (I am not sure why I installed it in the first place)?

I'll be glad to provide further details.

I also tried 64-bit binaries (rev. 1998, rhel-4-python-gtk2), but those
crash anytime I try to load an MTZ file (fftw: BUG in executor: invalid
plan).


-- 


Re: [COOT] ELFCLASS64

2009-05-11 Thread Paul Emsley

Ed Pozharski wrote:

After recent upgrade to Ubuntu 9.04, coot binaries that worked fine
before started reporting the ELFCLASS64 error when loading a
particular library, namely /usr/lib/libguile-srfi-srfi-1-v-3.so.3.  


I understand that the real root of this problem is my bizarre obsession
with installing 64-bit Linux and then being too lazy to compile coot
from source and instead trying to use 32-bit coot binaries.  To resolve
the ELFCLASS64 issue, I downloaded guile1.8 32-bit debian package from
ubuntu repositories and placed libraries into /usr/lib32.  That, of
course, didn't help and I had to redirect the symbolic link in /usr/lib
to /usr/lib32.  Now coot runs fine, but this is an ugly fix, not to
mention that it may cost me down the road when some 64-bit application
discovers that I substituted the library.  At the same time, I see that
$COOT_PREFIX/lib contains all the libraries, and so my question is why
coot tries to load libraries from /usr/lib?  Should I uninstall guile
via synaptic (I am not sure why I installed it in the first place)?



Very curious. AFAIU the libguile-srfi-srfi are loaded at runtime 
(probably for some string function).  I would have thought that they 
should load from the installation directory (rather than the system 
one).  How curious.  (And, yes, it is ugly.)


Well, I'll be over your way in a couple of weeks, if we don't get it 
sorted out now, we should try to find some time then.


Paul.


Re: [COOT] Graphics problem running Coot with EdUbuntu 8.10

2009-05-11 Thread Shaun Lott

Hi Stephen

On the money - thanks!

Running GNOME as the desktop environment, doing exactly as you suggest  
fixes the problem. GNOME was having other stability issues also, which  
caused some student frustration.


Alternatively, using Xfce as the desktop environment worked right off  
the bat.


I also tried KDE, and if anything it was worse than GNOME, plus I  
couldn't find where to disable Compiz.


Hope this helps anyone else who may have struggled with this issue.

cheers

Shaun

--
Dr J. Shaun Lott
AgResearch Senior Lecturer in Structural Biology
Laboratory of Structural Biology  Maurice Wilkins Centre
School of Biological Sciences
3a Symonds Street
University of Auckland
Private Bag 92019
Auckland 1142
New Zealand

t   : +64 9 3737599 x87074
f   : +64 9 3737416
http://shaunlott.blogspot.com

On 11 May 2009, at 17:51, Stephen Graham wrote:


Hi Shaun,

Have you tried turning off compiz?
(System  Preferences  Appearance  Visual Effects: Select 'None')

Cheers,

Stephen

On 11/05/2009, Shaun Lott s.l...@auckland.ac.nz wrote:

Hi

Apologies if this problem has been dealt with elsewhere - I scanned  
the

archives but couldn't see anything that looked similar.

I'm about to use Coot as part of a graduate teaching exercise.  
Version 0.52
starts ok, and can load co-ords and maps, but whenever one clicks,  
the
screen gets corrupted - see attached image. You can get a normal  
view back

by rotating the molecule, but the whole user experience is a pretty
frustrating one, as it is pretty much impossible to click on  
anything. The
fault seems to be hardware and Coot version independent - it  
manifests in

0.5.2 and also using
0.6-pre-1-revision-1997-binary-Linux-i686-ubuntu-8.04.2, though less
dramatically in the latter - just a grey screen rather than the  
corrupted
one. The same thing occurs when using a Dell or an iMac running  
Ubuntu

(don't ask...)

So I'm guessing it's a(n) Ubuntu thing. The machine are running the  
same

versrion of EdUbuntu 8.10, details as below.

Has anyone else seen this? Does anyone have a fix?

cheers

Shaun


cat /proc/version
Linux version 2.6.27-7-generic (bui...@palmer) (gcc version 4.3.2  
(Ubuntu

4.3.2-1ubuntu11) ) #1 SMP Tue Nov 4 19:33:20 UTC 2008






--
Dr Stephen Graham
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549