[phenixbb] Phenix version 1.7-650 and Pymol

Message: 11 Date: Mon, 31 Jan 2011 16:37:14 -0800 From: Nathaniel Echols To: PHENIX user mailing list Subject: Re: [phenixbb] Phenix version 1.7-650 and coot Message-ID: Content-Type: text/plain; charset=ISO-8859-1

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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

On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks wrote: 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:

unset XDG_DATA_DIRS

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

On 02/01/2011 04:20 AM, [email protected] wrote: 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, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741