Re: [COOT] problems running coot on an intel Imac 10.5.2

[William Scott]

Dear Stan, Len et al:

I want to apologize to the 10,000 or so who have emailed me about coot  
in the last couple of days. I've been working on a proposal and my  
children declared biological warfare on me, so I've been a bit slow  
about responding.  I hope you will forgive the blanket, impersonal  
reply.



I  have installed your 10.5 intel coot binary to run on my intel  
Imac using Fink.


When I source the program, the following error message appears:

dyld: Library not loaded: /usr/X11/lib/libXrandr.2.dylib
 Referenced from: /sw/bin/coot
 Reason: Incompatible library version: coot requires version 4.0.0  
or later, but libXrandr.2.dylib provides version 3.0.0

Trace/BPT trap

Is there an easy fix to this, or should I just go to the pub.


For coot on 10.5, I installed the latest X11 with the hope it would  
improve things, and this has newer versions of some libraries that get  
linked dynamically, which has caused many people some grief.


To get the newer X11, go here:

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

You can check to see if it is the right version this way:

otool -L /usr/X11/lib/libXrandr.dylib
/usr/X11/lib/libXrandr.dylib:
/usr/X11/lib/libXrandr.2.dylib (compatibility version 4.0.0,  
current version 4.0.0)


The Apple X11 guy is now working with coot to try to fix the bug that  
causes it to freeze or crash, and there will likely be a new release  
soon.  The problem is beyond my very limited abilities, I am afraid.


So start the download and then go to the pub.



I've been using your cootautoopener and have trouble with crosseye  
stereo.  using a ppc mac and a thin 20 inch diagonal screen, when i  
expand to a larger viewing area, the stereo images are not the same  
size.  i can sometimes use a work around by quitting and re-starting  
but this often doesn't work.


my screen currently is running at 1920 X1200.

any idea what i am doing wrong?


The auto-opener is just a wrapper for a shell script that starts coot  
for you, so that is probably a red herring.  Window resizing in the  
context of Apple's X11 is a bit buggy.  In my case, once I go into  
stereo mode, and then leave, I can no longer make the window any  
smaller.


I saw what you describe on linux once, but not OS X.  However, I've  
seen other weird stuff on OS  X that probably is due to the same bug.


The safest work-around in this case is to start coot without the auto- 
saved script, which will resize your window.  Size the window so that  
it is the desired size vertically and then 1/2 of the desired size for  
stereo horizontally, and then switch into the stereo mode. It should  
then do the right thing.  If you save the state and then re-start in  
mono, the window will be too large, so this is an irritation, but I  
can't think of a better way to deal with it.





Further notes:  I still haven't figured out hardware stereo on 10.5.  
Unfortunately I don't own such a machine, so I can't do a whole lot.




Bill

Re: [COOT] problems running coot on an intel Imac 10.5.2

[William Scott]

On Apr 9, 2008, at 11:35 AM, Stanley Moore wrote:

I installed the new version of X11, but unfortunately it doesn't  
seem to fix the problem.



My bad.

Go here:   http://xquartz.macosforge.org/downloads/

Install  X11-2.2.0_rc3.pkg

unless something more recent appears between now and when you read this.

Re: [COOT] problems running coot on an intel Imac 10.5.2

[Paul Emsley]

William Scott wrote:

The Apple X11 guy is now working with coot


interesting..!

to try to fix the bug that causes it to freeze or crash, and there 
will likely be a new release soon.  The problem is beyond my very 
limited abilities, I am afraid.


So start the download and then go to the pub.


Yes, I have that sort of internet connection too...





I've been using your cootautoopener and have trouble with crosseye 
stereo.  using a ppc mac and a thin 20 inch diagonal screen, when i 
expand to a larger viewing area, the stereo images are not the same 
size.  i can sometimes use a work around by quitting and re-starting 
but this often doesn't work.


Hmm... I just noticed this yesterday.  For me, the image on the right 
distorts, squeezed or pulled out (depending on how I resize) but after a 
few frames of rotation (rather than window resizing), it sorts itself 
out to the correct image. (That is on FC4).






The auto-opener is just a wrapper for a shell script that starts coot 
for you, so that is probably a red herring.  Window resizing in the 
context of Apple's X11 is a bit buggy.  


More than likely than not that it is not their bug, in this case.

In my case, once I go into stereo mode, and then leave, I can no 
longer make the window any smaller.


Oh dear.  Even after revision 946? (I think this is related to the bug 
that Ethan Merritt mentioned)


I saw what you describe on linux once, but not OS X.  However, I've 
seen other weird stuff on OS  X that probably is due to the same bug.


I have not seen it on OS X either (not surprising :)

The safest work-around in this case is to start coot without the 
auto-saved script, which will resize your window.  Size the window so 
that it is the desired size vertically and then 1/2 of the desired 
size for stereo horizontally, and then switch into the stereo mode. It 
should then do the right thing.


Yes...

If you save the state and then re-start in mono, the window will be 
too large, so this is an irritation, but I can't think of a better way 
to deal with it.


Not so, after the Ethan Merritt bug was fixed, is my thinking. ( Or is it?)

Further notes:  I still haven't figured out hardware stereo on 10.5. 
Unfortunately I don't own such a machine, so I can't do a whole lot.


Me neither, for the record. (And I have not yet managed to compile Coot 
on my 10.5 machine, and I think that that is Apple's showstopper).


Paul.