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