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 wrote:

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

Hi Nat, It looks like the crisis has been averted. One of my colleagues suggested that the problem could be due to running Phenix on our data processing server and when I tried to run it locally instead, the problem cleared up. Go figure. :p Thanks for your help regardless! Let me know if you would still like me to send any files in case it's something that you should know about. ~Brennan~ ________________________________________ From: [email protected] [[email protected]] On Behalf Of Nathaniel Echols [[email protected]] Sent: Wednesday, January 09, 2013 2:57 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Refining anomalous groups On Wed, Jan 9, 2013 at 12:51 PM, Brennan Bonnet wrote:

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)

Yuck. Just to make sure it's not a bug in our code, could you please send me the input PDB file (I don't need data)? I will try to reproduce the problem tomorrow. You might also want to consider trying a different installer; which one did you download? We do not have a Fedora 17 build yet, but maybe we should. -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi Nath, Happy 2013! Is it possible to use anomalous automatism also under GUI? Will be the event of refinement of anomalous dispersion parameters f' and f" recorded in PDB file? FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: [email protected] Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Jan 9, 2013, at 22:38 , Nathaniel Echols wrote:

On Wed, Jan 9, 2013 at 12:26 PM, Brennan Bonnet wrote:

...

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

Hello,

There's probably no reason why it needs to be this hidden - it seems very safe so far, but until we've had more chances to test it we prefer to minimize the number of features that can potentially break.

My understanding is that this option will select all atoms that are heavier than some defined value, and then it will refine f' and f'' for them. This may mean that you will be refining f' and f'' for atoms that were not anomalously scattering; that is you will be refining parameters that do not need to be refined. While this may be harmless (though someone needs to prove it) I believe it is suboptimal: 1) runtime wise, and 2) unnecessary refined parameters may mop up other model errors. Analogy could be: refining occupancy of fully occupied atoms.

...

Will be the event of refinement of anomalous dispersion parameters f' and f" recorded in PDB file? I am not sure whether phenix.refine includes anything in the headers -

It does output it like this: REMARK 3 ANOMALOUS SCATTERER GROUPS DETAILS. REMARK 3 NUMBER OF ANOMALOUS SCATTERER GROUPS : 2 REMARK 3 ANOMALOUS SCATTERER GROUP : 1 REMARK 3 SELECTION: name BR REMARK 3 fp : -0.8792 REMARK 3 fdp : 5.8029 REMARK 3 ANOMALOUS SCATTERER GROUP : 2 REMARK 3 SELECTION: name CO REMARK 3 fp : 0.0000 REMARK 3 fdp : 0.0000 but does not read. Pavel

Hi Felix,

Is the use of I+ I- with apparently larger impact on the final structure is not a sufficient justification?

yes, this is true. Did any one doubt it? If you know which atoms are anomalous scatterers and you have I+ and I- then it is a valid idea to refine their f' and f''. However, automatically making decision to refine f' and f'' just based on atom heaviness and presence of I+ and I- seems questionable to me. May be it's just fine but so far I haven't see logic and convincing arguments for doing this.

In structures with good diffraction data and sufficient resolution we frequently see S atoms on the anomalous difference map.

Sure. This is good knowledge sufficient to make decision to refine their f' and f''. Decisions about choice of refinement strategy and model parametrization have to be supported by the experimental data and model quality. In this case you know that your sulfurs are anomalous scatterers and you use this knowledge to decide refining their f' and f''. Pavel

Hi Felix,

However in may hands manual selection of anomalous scatterers for the refinement never worked. Well "never" is too strong. Couple of times I have tried I did not succeed.

I never heard a bug report or questions from you on this matter. I can't help without knowing what happened: "never worked" doesn't tell me a whole lot to either fix the problem (if it actually exists) or help you. So if there is a problem and you want me to address it, then please explain me what exactly it is and I will do all I can.

As you say, generally we can survive without this refinement,

No, I did not say this. Pavel