[phenixbb] Phenix version 1.7-650 and Pymol
bene at hkl.hms.harvard.edu
Wed Feb 2 12:42:24 PST 2011
On Wed, Feb 02, 2011 at 12:09:20PM -0500, Leonid Flaks wrote:
> >On Tue, Feb 1, 2011 at 5:49 AM, Leonid Flaks<flaks at bnl.gov
> ><http://phenix-online.org/mailman/listinfo/phenixbb>> wrote:
> >>/ Nat, As I reported minutes ago coot issue is solved. Now I clicked on
> />>/ 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
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:
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
| Ben Eisenbraun
| SBGrid Consortium | http://sbgrid.org |
| Harvard Medical School | http://hms.harvard.edu |
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