[phenixbb] Phenix.ensemble_refinment questions

[Tim Gruene]

Dear Mark,

for a 1A structure, at least when it is near completeness, I would
expect the phase information from the model much, much more accurate
than from a SAD experiment, i.e. I'd rather expect the R value to get
worse when you include SAD phasing information. For example, when
developers show the phase errors of their methods for phasing
experiments, the error is generally calculated with respect to the final
model.

Did you observe the drop at an early stage of refinement with a low
complete model?

Regards,
Tim

On 11/13/2014 05:03 PM, Mark Wilson wrote:
> Hi All,
> As I am (I think) the other user that Nat is referring to, I'll comment.
> I requested support for experimental phase information in the PHENIX
> ensemble refinement target and can verify that it is accepted (in my case
> as HL coeffs) and will run.  The result in my test case was not
> dramatically different than an amplitude-based target, but obviously a
> great many factors could affect this.  What differences I saw were minor
> improvements in R/Rfree (~1%) with Se-Met SAD phases in a 1.05 Å
> resolution structure of a flexible protein.  I've not dug too much more
> into this, but I can verify that phases are accepted and do influence the
> final ensemble.
> Best regards,
> Mark
> 
> Mark A. Wilson
> Associate Professor
> Department of Biochemistry/Redox Biology Center
> University of Nebraska
> N118 Beadle Center
> 1901 Vine Street
> Lincoln, NE 68588
> (402) 472-3626
> mwilson13 at unl.edu 
> 
> 
> 
> 
> 
> On 11/13/14 9:53 AM, "Nathaniel Echols" <nechols at lbl.gov> wrote:
> 
>> On Thu, Nov 13, 2014 at 6:46 AM, Joseph Brock <joseph.brock at ki.se> wrote:
>>
>> 1. In the associated publication (Burnley et
>> al. eLife 2012;), the ensemble refinement is validated by comparing the
>> correlation of the ensemble generated map, with the map generated
>> from the experimental phases for PDB entry 1YTT... I am confused how one
>> computes an experimentally phased from structure factors deposited in the
>> PDB that contain only anomalous intensities/amplitudes and not
>> Hendrickson-Lattman
>> coefficients. Is there a program within the phenix package that can do
>> this?
>>
>>
>>
>>
>>
>>
>> AutoSol can be used to re-solve such datasets, although in the case of
>> 1YTT it requires additional information that wasn't deposited.
>>
>>
>> Is it possible to include experimental phases during the rolling average
>> refinement process and could this be beneficial (if the phases were of a
>> sufficient quality)?
>>
>>
>>
>>
>>
>>
>> It is possible, but completely untested aside from verifying that it
>> doesn't crash.  I added this a year ago at the request of another user
>> but haven't looked into it since.
>>
>>
>>
>> 3. What is the function of the "nproc" keyword? If this is the number of
>> CPU cores that can be used in parallel, what is the most efficient way of
>> using phenix.ensemble_refinement on a cluster?
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> The only parallelization is in the optimization of the ptls parameter -
>> i.e. if you try N values for ptls, you can run N jobs at once.  For a
>> single ptls it will run in serial.  So on a cluster, you are better off
>> running N different jobs separately.
>>
>>
>>
>> Finally, I noticed that I cannot run phenix.ensemble_refinement using a
>> "my_parameters.eff" file, it is necessary to type on the command line.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> That sounds like a bug...
>>
>>
>> -Nat
>>
>>
>>
> 
> 
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-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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