[phenixbb] Phenix version 1.7-650 and coot

Leonid Flaks flaks at bnl.gov
Mon Jan 31 06:57:14 PST 2011

On 01/29/2011 03:00 PM, phenixbb-request at phenix-online.org wrote:
> Message: 1
> Date: Fri, 28 Jan 2011 12:09:01 -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:
> 	<AANLkTini0jaSAh9KKv1xZGbtE4ABtdU2_G5KMxWP0c4p 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:
>> 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'
>> for png and svg files in the console window. I can see all of the icons if I
>> start coot directly. I am using coot version 1.6.2-pre1 rev 3213 which is
>> installed on 64-bit fedora 14 as a rpm file. I did not see this issue on a
>> phenix version 1.6.4-476 with the same version of coot.
> Could you please send me the complete console output from Coot under
> these conditions:
> a) when launching from Phenix 1.7
> b) when launching from Phenix 1.6.4
> c)when launching from the command line?
> Very little has changed in the Coot-related parts of Phenix since
> 1.6.4, so I'm not sure how it's possible for one to work but not the
> other.  In the past, errors like this were due to conflicts with the
> shared libraries distributed with Phenix, but we largely reset the
> environment when starting Coot to avoid the problem, and I'm pretty
> sure we started that a year and a half ago.
> thanks,
> Nat
Nat, first of all - my apologies for the incorrect report. It turned out 
this problem exists in phenix 1.6.4 under fedora 14 also - just nobody 
noticed it on the current setup! Fedora 14 is about 2 month old and we 
are coming out of  the winter shutdown. We had a mixture of fedora 12 
and 13 before and did not see that problem. Of course, python version 
has been changed to python-2.7 for Fedora 14.
Console output for all 3 conditions are saved. I'll mail them to you 
directly - I don't want to flood the list.




Leonid Flaks

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

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