[phenixbb] Phenix version 1.7-650 and Pymol

Leonid Flaks flaks at bnl.gov
Tue Feb 1 05:49:14 PST 2011

On 02/01/2011 04:20 AM, phenixbb-request at phenix-online.org wrote:
> Message: 11
> Date: Mon, 31 Jan 2011 16:37:14 -0800
> From: Nathaniel Echols<nechols at lbl.gov>
> To: PHENIX user mailing list<phenixbb at phenix-online.org>
> Subject: Re: [phenixbb] Phenix version 1.7-650 and coot
> Message-ID:
> 	<AANLkTim6ux3V6FcfhXr_0vhNf2P9GWXfBh3aexbZcZ41 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks at bnl.gov>  wrote:
>> >  Hi!
>> >  I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that
>> >  if I start coot from within phenix interface, most of the icons on the right
>> >  hand side of the coot window are not displayed.
>> >  There is a lot of messages like this:
>> >
>> >  Error loading icon: Couldn't recognize the image file format for file
>> >  '/usr/share/coot/pixmaps/residue-info.png'
> Okay, apparently we missed an important environment variable in the
> script that launches Coot from Phenix - several library paths need to
> be cleansed to prevent conflicting with the libraries we distribute.
> The one we didn't know about (because it never caused problems before)
> appears to be XDG_DATA_DIRS.  The crude fix for this is to edit
> $PHENIX/phenix/phenix/command_line/start_coot.sh and add this line at
> the end of a list of "unset" commands:
> It'll be fixed in the next build too.  If this doesn't totally solve
> the problem, let me know - I'm going to unset several other paths too,
> but those didn't appear to have any effect on our Fedora 14 machine.
> -Nat
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

So, looks like we need to unset more variables indeed ;-)
Meanwhile I'll just keep clicking on buttons...

All the best,



Leonid Flaks

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

More information about the phenixbb mailing list