Hi Brennan, I'm sorry, part of the problem is that autosol exptl_fobs_phases_freeR_flags_1.mtz file does not retain the anomalous information. This is now on my list be fixed (not quickly though because I will be able to do it only when I convert a whole lot of other things). So in your case the best thing is to run phenix.refine with your original mtz file. You can create a freeR set in the GUI. If you do this, then use your new freeR set for everything from now on. As Nat mentions, if you choose "F(+),SIGF(+),F(-),SIGF(-)" or something like it then it should work. All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Brennan Bonnet [[email protected]] Sent: Monday, November 19, 2012 8:03 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Refining Anomalous Groups Ok. So I used the original mtz file created from my data to determine the heavy atom substructure using HySS which I then used as input for AutoSol. Next I carried the files through to AutoBuild these files are: exptl_fobs_phases_freeR_flags_1.mtz (experimental data) resolve_1.mtz (initial map) overall_best_placed.pdb (ligands, starting model) ha_1.pdb_formatted.pdb (heavy-atom sites) Finally I carried these through to phenix.refine and now is when it complains that my data is no longer anomalous and I can't find a file that phenix is happy with. Everything worked smoothly until this step. Any idea what file(s) I might be looking for? I have tried some data from earlier steps which are unmerged and it still complains. ~Brennan~ From: [email protected] [[email protected]] On Behalf Of Nathaniel Echols [[email protected]] Sent: Monday, November 19, 2012 8:29 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Refining Anomalous Groups On Mon, Nov 19, 2012 at 6:11 PM, Brennan Bonnet mailto:[email protected]> wrote: I am trying to use phenix.refine to refine partially occupied xenon sites using the Anomalous Groups selection under "Refinement settings". My list of anomalous scatters initially consisted of 22 peaks as located by HySS. Some of these were removed as they originated from S atoms from Met and Cys residues and a few others were removed after previous refinement steps due to having zero occupancy. My remaining sites consist of my xenons (hopefully) and other metals such as Mg or Zn which are mixed in and look like partially occupied xenon sites. My problem is that when I try to define the 11 remaining sites for the "refine anomalous groups" selection the software complains: Invalid combination: F-obs not anomalous, but refinement of 11 f_double_prime values requested (11 scatterers): Please provide anomalous reflection data or fix all f_double_prime values (see refinement.refine.anomalous_scatterer.group input blocks) I can't figure out exactly what I need to change to make it work and can't find a guide anywhere. Do I need to provide additional data or is the syntax for the sites incorrect maybe? No, the error message means exactly what it says: you need to supply anomalous data as input. This almost always means that the selected data labels should have "+" and "-" in them, and there will usually be 4 labels (e.g. "F(+),SIGF(+),F(-),SIGF(-)"). Data named "F,SIGF", on the other hand, is almost always merged/non-anomalous (although I think CNS files may break this assumption). -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Hi Nat, Yes, you're right (I forgot). For autosol runs with SAD data and where remove_aniso=True, a file exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz is created with the original anomalous data is created. This is suitable for refinement. And also yes, you're right that it is much better to copy the freeR flags instead of creating a new set which could cause a lot of confusion later. All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Nathaniel Echols [[email protected]] Sent: Monday, November 19, 2012 10:52 PM To: PHENIX user mailing list Subject: Re: [phenixbb] Refining Anomalous Groups On Mon, Nov 19, 2012 at 7:47 PM, Terwilliger, Thomas C mailto:[email protected]> wrote: I'm sorry, part of the problem is that autosol exptl_fobs_phases_freeR_flags_1.mtz file does not retain the anomalous information. This is now on my list be fixed (not quickly though because I will be able to do it only when I convert a whole lot of other things). But doesn't AutoSol write another MTZ file that is anomalous? In one of my directories I have this: exptl_fobs_phases_freeR_flags_1_with_anom_data_with_hl_anom.mtz which definitely has F+ and F-. (I'm not certain whether this actually appears in the GUI or not - if not, sorry, that's a bug. And it may not be propagated to other programs either, which could also be misleading.) So in your case the best thing is to run phenix.refine with your original mtz file. You can create a freeR set in the GUI. I wouldn't recommend creating a new test set - it is just as easy to combine the anomalous data from the original MTZ file with the R-free flags from exptl_fobs_phases_freeR_flags_1.mtz in the reflection file editor. -Nat