After I updated OsX 10.2.8 to 10.3.1 pymol is not longer working with X11 (I know there is aqua version of pymol). I had installed pymol using the using the version 0.5 of fink,, and nowI am on the version 0.6.2.cvs. This is what I get when I issue the command pymol from Xterm.
Traceback (most recent call last):
File "/sw/lib/pymol/modules/pymol/__init__.py", line 93, in ?
import pymol
File "/sw/lib/pymol/modules/pymol/__init__.py", line 236, in ?
import _cmd
ImportError: Failure linking new module: : dyld: /sw/bin/python Undefined symbols:
_glBegin
_glBlendFunc
_glClear
_glClearColor
_glColor3f
_glColor3fv
_glColor3ub
_glColor4f
_glColor4ub
_glColorMaterial
_glDisable
_glDrawBuffer
_glDrawPixels
_glEnable
_glEnd
_glFlush
_glFogf
_glFogfv
_glGetFloatv
_glGetIntegerv
_glGetString
_glHint
_glLightModelfv
_glLightModeli
_glLightfv
_glLineWidth
_glLoadIdentity
_glMaterialfv
_glMatrixMode
_glMultMatrixf
_glNormal3fv
_glOrtho
_glPointSize
_glPopMatrix
_glPushMatrix
_glRasterPos3i
Line line 93 in __init__.py reads "import pymol". Neither pymol.py or pymol.pyc is anywhere in my computer. Line 236 reads "import _cmd, and I have in the directory where __init__.py is located (/sw/lib/pymol/modules/pymol) the file _cmd.so and cmd.py and cmd.pyc.
The executable pymol is a csh script located in /sw/bin/ and is as it follows:
#!/bin/csh -f
#
# PyMOL startup script
#
# ==============================================================
# Set PYMOL_PATH to point at the correct location on your system
#
setenv PYMOL_PATH /sw/lib/pymol
#
# ==============================================================
# (no changes usually required below here)
#
setenv PYMOL_EXTLIBPATH /sw/lib
#
# Tcl/Tk path
setenv TCL_LIBRARY /sw/lib/tcl
#
# dynamic linking
#
if ( $?LD_LIBRARY_PATH ) then
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${PYMOL_EXTLIBPATH}
else
setenv LD_LIBRARY_PATH ${PYMOL_EXTLIBPATH}
endif
#
# python modules
#
if ( $?PYTHONPATH ) then
setenv PYTHONPATH ${PYMOL_PATH}/modules:${PYMOL_EXTLIBPATH}/python2.2:${PYTHONPATH}
else
setenv PYTHONPATH ${PYMOL_PATH}/modules:${PYMOL_EXTLIBPATH}/python2.2
endif
#
#
#dbx $PYMOL_PATH/ext/bin/python
#gdb $PYMOL_PATH/ext/bin/python
#$PYMOL_PATH/ext/bin/python $PYMOL_PATH/modules/launch_pymol.py $*
/sw/bin/python $PYMOL_PATH/modules/pymol/__init__.py $*
I have tried to update and reinstall pymol but the command fink update pymol or find install pymol gives me the following:
Information about 1119 packages read in 1 seconds. No packages to install.
However if I do fink list pymol I got the follwoing:
i pymol 0.86-13 Molecular graphics system
I thought of doing fink purge pymol and then fink install pymol, but I am scared of messing things up, thus any help for making pymol to work again with X11 with appreciated. I have tow python version. That in /sw/bin es 2.2.3 and that in /usr/bin/ is 2.3
Cheers
======================================================================== ======
Pedro A Reche, PhD
MIF Bioinformatics Group Head
Dana-Farber Cancer Institute (D1510A) TL: 617 632 3824
Harvard Medical School FX: 617 632 3351
44 Binney Street , EM: [EMAIL PROTECTED]
Boston, MA 02115, USA W3: www.mifoundation.org
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