[phenixbb] MR-SAD, SAD

Randy Read rjr27 at cam.ac.uk
Mon Jan 26 07:32:45 PST 2015


This rms value is used to calculate the initial values of some error estimates for structure factors from the partial model as a function of resolution, which are then refined.  After those error estimates are refined, they will account for a combination of incompleteness and coordinate error.

The default value of 1A is going to be fine most of the time, because the refinement will converge most of the time from the initial values computed from this.  However, if you want to you can look at what the MR step in Phaser estimated as the RMS error of the model after the final refinement (the refined VRMS value at the bottom of the log file) and give that number instead.

Best wishes,


On 26 Jan 2015, at 15:19, Terwilliger, Thomas Charles <terwilliger at lanl.gov> wrote:

> Hi Francis,
> An estimated RMSD is used in the calculation in Phaser.  You can specify 
>   partpdb_rms = 1
> to define the estimated RMSD between model and true structure that is used when Phaser is called by autosol.  The default is 1 A.  I think there is no way at present to tell Phaser about incompleteness, at least autosol does not have a keyword for it (Randy may be able to comment on that...)
> All the best,
> Tom T
> ________________________________________
> From: Francis Reyes [reyesf at colorado.edu] on behalf of Francis Reyes [Francis.Reyes at Colorado.EDU]
> Sent: Monday, January 26, 2015 8:13 AM
> To: Terwilliger, Thomas Charles
> Cc: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] MR-SAD, SAD
> Hi Tom,
> How is the input MR model treated when computing the HL's for the substructure search?
> That is to say, how are errors in the MR solution taken into account or is the input model treated as being correct?
> Errors being: positional errors, or model incompleteness errors?
> Thanks,
> F
> On Jan 25, 2015, at 3:06 PM, Terwilliger, Thomas Charles <terwilliger at lanl.gov> wrote:
>> If everything were ideal, then an MR solution, even if very distant and contributing very little phase information, should improve the Phaser identification of the sub-structure.  Therefore as you imagine, including it should have improved the situation.  In real life there is a lot of noise in the system, so small changes can sometimes make the difference between finding sites and not. Also the default parameters for Phaser sub-structure identification are not exactly the same for MR-SAD and for extreme defaults in autosol.
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
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Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk

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