Cross Validation Reflection Set question
Dear All, Here is the situation, I have data to 2 A. I refined the model to 3 A first with S.A. Now I want to use higher res data for the rest of refinement. My Rfree created in the first round when I only used data to 3A. Was Rfree set created using all the data or just up to 3A shell? or do I have to extend into higher res shells? one caviot is I had twin law h,-k,-h-l enabled when they were created. Thanks, -- Yuri Pompeu
On Sun, Nov 6, 2011 at 4:28 PM, Yuri
Here is the situation, I have data to 2 A. I refined the model to 3 A first with S.A. Now I want to use higher res data for the rest of refinement. My Rfree created in the first round when I only used data to 3A. Was Rfree set created using all the data or just up to 3A shell? or do I have to extend into higher res shells?
I just tried doing this, and it looks like the R-free flags will cover the full resolution range, at least with the current code. You can verify this by running phenix.mtx.dump on the output MTZ file, or in the GUI, click the magnifying glass icon next to the file name and it will pop up an info panel.
one caviot is I had twin law h,-k,-h-l enabled when they were created.
That shouldn't matter, as long as you told it to take lattice symmetry into account when creating the flags (use_lattice_symmetry=True, which is the default - I'm not sure why this is even optional). -Nat
Here is the situation, I have data to 2 A. I refined the model to 3 A first with S.A.
Is this really necessary in this case (refine against lower res data, then continue with the whole data set)? I can see why it may be good to do if you say have 0.7A resolution data set and you just solved a MR problem and have Rs~40%, then yes, getting some more or less good model using ~2A data is a good first step before jumping into modeling finer details using all data.
(use_lattice_symmetry=True, which is the default - I'm not sure why this is even optional).
To be able to prove that it is a good idea. Pavel
participants (3)
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Nathaniel Echols -
Pavel Afonine -
Yuri