Re: [COOT] coot for 10.4 and 10.5 intel
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] coot for 10.4 and 10.5 intel
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] coot for 10.4 and 10.5 intel
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] coot for 10.4 and 10.5 intel
On Fri, December 12, 2008 10:12 am, Nathaniel Echols wrote: > On Thu, Dec 11, 2008 at 3:05 AM, William Scott > wrote: > >> I need a couple of people to volunteer to test this on 10.4 and 10.5 >> intel >> machines: >> >> http://sage.ucsc.edu/xtal/coot/coot-0.5-pre1-intel_10.4_10.5.tgz >> > > This build appears to have python embedded more or less correctly, so it > now > uses the built-in interpreter when launched with "--script test.py": > > coot-0.5: > sys.executable = /Users/nat/phenix/build/bin/python > > coot-0.5-pre1: > sys.executable = /usr/local/xtal/coot/bin/coot-real > > I wish I knew what the difference in the builds was. . . I'm going to try > the fink version next. > > Unfortunately, there appear to be problems with the actual Python modules. > I'm not entirely sure what specifically is broken, but I have to manually > add /usr/local/xtal/coot/share/coot/python to sys.path, and the module > formerly known as coot_python does not appear to exist any more (but is > still referenced in several places). So it doesn't look like it's > possible > to manipulate the GUI from Python right now, although this is clearly a > step > in the right direction. [I can send more info to Paul/Bernhard off-list > if > this isn't a known problem.] > > thanks, > Nat > I built it naively, and using fink, according to the following: http://sage.ucsc.edu/~wgscott/xtal/wiki/index.php/Building_a_stand-alone_coot_on_OS_X >From what I have seen, python within coot no longer is aware of what is in the site-packages directory. I guess sys.path is getting clobbered somehow, but I don't understand how python is implemented in coot, so I don't have anything useful to suggest. If someone smarter than me can suggest a fix, I will immediately implement it. Thanks. Bill William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [COOT] coot for 10.4 and 10.5 intel
On Thu, Dec 11, 2008 at 3:05 AM, William Scott wrote: > I need a couple of people to volunteer to test this on 10.4 and 10.5 intel > machines: > > http://sage.ucsc.edu/xtal/coot/coot-0.5-pre1-intel_10.4_10.5.tgz > This build appears to have python embedded more or less correctly, so it now uses the built-in interpreter when launched with "--script test.py": coot-0.5: sys.executable = /Users/nat/phenix/build/bin/python coot-0.5-pre1: sys.executable = /usr/local/xtal/coot/bin/coot-real I wish I knew what the difference in the builds was. . . I'm going to try the fink version next. Unfortunately, there appear to be problems with the actual Python modules. I'm not entirely sure what specifically is broken, but I have to manually add /usr/local/xtal/coot/share/coot/python to sys.path, and the module formerly known as coot_python does not appear to exist any more (but is still referenced in several places). So it doesn't look like it's possible to manipulate the GUI from Python right now, although this is clearly a step in the right direction. [I can send more info to Paul/Bernhard off-list if this isn't a known problem.] thanks, Nat
Re: [COOT] coot for 10.4 and 10.5 intel
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
Re: [COOT] coot for 10.4 and 10.5 intel
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. ---
