[phenixbb] Phenix version 1.7-650 and Pymol

Ben Eisenbraun 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 
> >>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


| Ben Eisenbraun
| SBGrid Consortium                          | http://sbgrid.org       |
| Harvard Medical School                     | http://hms.harvard.edu  |

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