[phenixbb] Phenix version 1.7-650 and Pymol

Leonid Flaks flaks at bnl.gov
Wed Feb 2 13:02:04 PST 2011

On 02/02/2011 03:42 PM, Ben Eisenbraun wrote:
> 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
> 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 
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,



Leonid Flaks

Phone: (631) 344-2682
Fax  : (631) 344-2741

More information about the phenixbb mailing list