On Wed, Feb 02, 2011 at 12:09:20PM -0500, Leonid Flaks wrote:
On Tue, Feb 1, 2011 at 5:49 AM, Leonid Flaks
http://phenix-online.org/mailman/listinfo/phenixbb> wrote: / Nat, As I reported minutes ago coot issue is solved. Now I clicked on pymol />>/ button - got an error: />>/ />/> /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe: error while loading />/> shared libraries: libXmu.so.6: cannot open shared object file: No such file />>/ or directory /> That's a system library, and not something we distribute or otherwise interfere with. Does PyMOL even work on the command line? Nat, pymol is installed as rpm binary and works fine from command line. The library in question is also installed from rpm:
dunkin:/home/pxuser 104: rpm -qf /usr/lib64/libXmu.so.6 libXmu-1.0.5-2.fc13.x86_64 Nat is talking about a different PyMOL. The binary at /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe generated the error, but you're showing the info for one installed from YUM.
In any case, the problem is that the PyMOL shipped _with_ PHENIX is a 32-bit binary, even in the 64-bit download.
$ file phenix-1.7-650/pymol/pymol.exe phenix-1.7-650/pymol/pymol.exe: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV), for GNU/Linux 2.2.5, dynamically linked (uses shared libs), for GNU/Linux 2.2.5, not stripped
And the libXmu.so.6 that you have is 64-bit.
On my 64-bit Fedora 13 machine, the 32-bit libXmu is installed in /usr/lib and provided by libXmu-1.0.5-2.fc13.i686. Something similar should work for you. You may well have to run:
ldd /usr/local/crys/64/phenix-1.7-650/pymol/pymol.exe
And slowly install all the necessary 32-bit X11 libraries until you get it running in order for it to work.
I got a window on my OS X machine the other day telling me that PHENIX would prefer to use a newer MacPyMOL if it could find one in /Applications. Can I configure this to find the newer MacPyMOL in a different path? How about on linux? That might be another possible solution to Leonid's problem.
-ben
-- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu | Ben, thanks! That was it! Should have though of it myself ;-( I installed the 32-bit version of this library and it was enough. Of course the version of PyMOL from rpm is 1.3, which is much newer then
On 02/02/2011 03:42 PM, Ben Eisenbraun wrote: the one that phenix has (0.99-rc6) so I agree that it would be nice for phenix to see the other version installed before firing up the version that comes with it. Thanks again, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741