Still can't get refinement of anomalous groups to work
Hi all, I'm still working on this pesky anomalous group refinement problem. Originally, the problem was that the output from AutoBuild no longer retained the anomalous data. To fix this, I used the Phenix reflection file editor and combined exptl_fobs_phases_freeR_flags.mtz (which is automatically entered as input when running phenix.refine from AutoBuild) with the F+ F- values from my original reflection data. Now when I try to run refinement I get this error message: "This model appears to have previously been refined against a different set of R-free flags. Please resolve the mismatch." I find this strange since I am only modifying the file that phenix.refine tries to use anyway. How do I fix this problem? Thanks, ~Brennan~
On Wed, Jan 16, 2013 at 2:34 PM, Brennan Bonnet
I'm still working on this pesky anomalous group refinement problem. Originally, the problem was that the output from AutoBuild no longer retained the anomalous data. To fix this, I used the Phenix reflection file editor and combined exptl_fobs_phases_freeR_flags.mtz (which is automatically entered as input when running phenix.refine from AutoBuild) with the F+ F- values from my original reflection data. Now when I try to run refinement I get this error message:
"This model appears to have previously been refined against a different set of R-free flags. Please resolve the mismatch."
I find this strange since I am only modifying the file that phenix.refine tries to use anyway. How do I fix this problem?
There are several different reasons why this could happen, mostly having to do with the fact that the reflection file editor will extend your flags to cover all reflections. My guess is that the exact set of reflections changes slightly when you transfer the anomalous data, and the flags are therefore different. (I don't think you're doing anything wrong - it is very easy to get this error message accidentally, but it also catches some genuine mistakes, so it's quite valuable.) Just click the "Options" button in the "X-ray data and experimental phases" section, set the user level to "Advanced", and look for the control labeled "Ignore PDB hexdigest sanity check". This probably belongs in the FAQs... -Nat
Thanks Nat that takes care of that problem.
The new error message that I get is:
mlhl target function (maximum likelihood with experimental phases) currently not supported in combination with anomalous scattering
~Brennan
________________________________________
From: [email protected] [[email protected]] On Behalf Of Nathaniel Echols [[email protected]]
Sent: Wednesday, January 16, 2013 4:44 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Still can't get refinement of anomalous groups to work
On Wed, Jan 16, 2013 at 2:34 PM, Brennan Bonnet
I'm still working on this pesky anomalous group refinement problem. Originally, the problem was that the output from AutoBuild no longer retained the anomalous data. To fix this, I used the Phenix reflection file editor and combined exptl_fobs_phases_freeR_flags.mtz (which is automatically entered as input when running phenix.refine from AutoBuild) with the F+ F- values from my original reflection data. Now when I try to run refinement I get this error message:
"This model appears to have previously been refined against a different set of R-free flags. Please resolve the mismatch."
I find this strange since I am only modifying the file that phenix.refine tries to use anyway. How do I fix this problem?
There are several different reasons why this could happen, mostly having to do with the fact that the reflection file editor will extend your flags to cover all reflections. My guess is that the exact set of reflections changes slightly when you transfer the anomalous data, and the flags are therefore different. (I don't think you're doing anything wrong - it is very easy to get this error message accidentally, but it also catches some genuine mistakes, so it's quite valuable.) Just click the "Options" button in the "X-ray data and experimental phases" section, set the user level to "Advanced", and look for the control labeled "Ignore PDB hexdigest sanity check". This probably belongs in the FAQs... -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Wed, Jan 16, 2013 at 3:06 PM, Brennan Bonnet
The new error message that I get is:
mlhl target function (maximum likelihood with experimental phases) currently not supported in combination with anomalous scattering
Right, you need to uncheck the box labeled "Use experimental phases". I wasn't actually aware of this restriction until a few days ago, so the GUI doesn't automatically catch it (yet). -Nat
Hi Nat,
I'm assuming you mean the "use experimental phase restraints" option which is checked by default. The toggle is funny because in addition to checked and unchecked, there is a third option that looks like a dash in a box.
Now that you say it was a few days ago, I had a hunch that since you just became aware of this that it might have been fixed. I tried again using the latest nightly build on my personal computer and it's going.
Thanks for your help once again!
~Brennan
________________________________________
From: [email protected] [[email protected]] On Behalf Of Nathaniel Echols [[email protected]]
Sent: Wednesday, January 16, 2013 5:13 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] Still can't get refinement of anomalous groups to work
On Wed, Jan 16, 2013 at 3:06 PM, Brennan Bonnet
The new error message that I get is:
mlhl target function (maximum likelihood with experimental phases) currently not supported in combination with anomalous scattering
Right, you need to uncheck the box labeled "Use experimental phases". I wasn't actually aware of this restriction until a few days ago, so the GUI doesn't automatically catch it (yet). -Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
On Wed, Jan 16, 2013 at 3:34 PM, Brennan Bonnet
I'm assuming you mean the "use experimental phase restraints" option which is checked by default. The toggle is funny because in addition to checked and unchecked, there is a third option that looks like a dash in a box.
This usually means "figure out what to do automatically" - it's probably not relevant to the GUI in this case (especially since I've changed the way that box and the target function menu interact), but there are other controls elsewhere that have the same behavior. -Nat
participants (2)
-
Brennan Bonnet -
Nathaniel Echols