Hi,
I apologize, Phenix does not attempt to open Coot at this point but it does attempt to open some sort of viewing program which causes Phenix to crash.
I am running Fedora 17 and Phenix 1.8.1-1168
The only error message given is: Segmentation fault (core dumped)
~Brennan~
________________________________________
From: [email protected] [[email protected]] On Behalf Of Nathaniel Echols [[email protected]]
Sent: Wednesday, January 09, 2013 2:38 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Refining anomalous groups
On Wed, Jan 9, 2013 at 12:26 PM, Brennan Bonnet
I hope everyone had relaxing holidays to begin the new year. I am back to work trying to refine anomalous groups using phenix.refine.
I have managed to merge my files so that my exptl_fobs_phases_flags_1_with_hl_anom.mtz now contains F(+), SIGF(+), F(-), SIGF(-).
Now I have a new problem which was not occurring before the break. Usually I check the box for "Anomalous groups", then select "Modify selections for: Anomalous groups" which brings up a screen for atom selection and definition of f' and f''. In the past, clicking on the View/pick button launches Coot for selection of the atoms. Sadly, now clicking on the View/pick doesn't launch Coot and instead crashes Phenix.
What OS (including version) are you using, which Phenix installer did you use (including the exact package name), and could you please send me any error messages printed to the console? The built-in graphics is spectacularly difficult to get working on some Linux systems, for reasons I still don't understand. However, I don't think those buttons ever launched Coot - maybe something that looks superficially similar, perhaps, but it's obviously stopped working on your computer. I do have a suggestion for working around this, but it's a pain to use: a few weeks ago I added an option to set up the anomalous groups automatically. You have to choose the "Edit parameters and run" option when starting phenix.refine, then look for this parameter (heavily condensed): refinement { group_anomalous { find_automatically = False } } Change that to True, and every atom heavier than P will be treated as a separate anomalous group. (This is not necessarily the optimal way to do it, which is why it's hidden right now, but it worked well for the tests I've done so far.) -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb