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 [[email protected]] on behalf of Francis Reyes [[email protected]]
Sent: Monday, January 26, 2015 8:13 AM
To: Terwilliger, Thomas Charles
Cc: [email protected]
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
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.