On Jun 5, 2009, at 9:53 PM, William Scott wrote:
Two more thoughts:
1. What shell are you using? if it is tcsh, then you need to
source a different file, i.e.,
source /usr/local/xtal/coot/bin/init.csh
This solved it. However....
I am in fact using tcsh, just as I was on my previous Mac. On the
previous Mac the standard sourcing of the init.sh file did not raise
any issues though so tcsh is not the only culprit. Being a lazy
person, I wanted to then correct the coot wrapper script to reflect my
shell requirements so that I can invoke coot with only one command. In
the end this worked: (the script has only 6 lines, so be careful if
you copy and paste it as the wrapped lines may have copied as new
lines.)
#!/bin/csh -f
source /usr/local/xtal/coot/bin/init.csh
setenv COOT_REFMAC_LIB_DIR /usr/local/xtal/coot/share/coot/lib
setenv COOT_PYTHON_DIR /usr/local/xtal/coot/share/coot/python
setenv PYTHONPATH /usr/local/xtal/coot/lib/python25.zip:/usr/local/
xtal/coot/lib/python2.5:/usr/local/xtal/coot/lib/python2.5/plat-
darwin:/usr/local/xtal/coot/lib/python2.5/plat-mac:/usr/local/xtal/
coot/lib/python2.5/plat-mac/lib-scriptpackages:/usr/local/xtal/coot/
lib/python2.5/lib-tk:/usr/local/xtal/coot/lib/python2.5/lib-dynload:/
usr/local/xtal/coot/lib/python2.5/site-packages:/usr/local/xtal/coot/
lib/python2.5/site-packages/Numeric:/usr/local/xtal/coot/lib/python2.5/
site-packages/gtk-2.0:/usr/local/xtal/coot/share/coot/python
/usr/local/xtal/coot/bin/coot-real
Bill, perhaps you can tell me if my having removed the "$@" and
$PYTHONPATH in the original wrapper will be a problem down the line.
Since my environment does not have a pre-existing $PYTHONPATH, the
script would abort at this line when it was included. I suppose there
is a better syntax for the script that would allow for the possibility
of a $PYTHONPATH... but it is beyond me.
Thanks to all who responded with their input.
-Jason
because the syntax is not compatible with the other shells.
2. Maybe updating to the most recent X11 will help:
http://xquartz.macosforge.org/trac/
Sometimes Apple's updates will clobber parts of this, and regress it
to older versions of some files, which makes a mess, so if in doubt,
it is always a good idea to reinstall X11. I try to compile these
things with the most current X11, which might lead to
incompatibilities.
HTH,
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Jun 5, 2009, at 9:54 AM, Jason Greenwald wrote:
Thank you Bill and also other helpful folks.
I should have mentioned this my original post, but when I issue the
source command (which of course is also done by the coot wrapper
shell script) I get the result: "Illegal variable name." And coot
still does not work.
Perhaps something that is also of interest is that a handful of the
icons are visible in the graphics window:
Clear pending picks
Delete item
Recover session
Map color
Bond color
Background color
Preferences
About
and a few others. However, some others have an "x" icon (like for
a missing image while many (the majority?) others simply have
nothing to replace the missing icon.
In the meantime I am using the COOT.app package from the CCP4
download site, so if anyone knows how to save more than one session
using this installation, I would be happy to hear it.
Cheers.
Jason
On Jun 5, 2009, at 6:35 PM, William G. Scott wrote:
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
