[phenixbb] (no subject)

Nathaniel Echols nechols at lbl.gov
Thu Oct 2 08:12:19 PDT 2014

On Thu, Oct 2, 2014 at 7:34 AM, Sneha Rangarajan <rsneha at umd.edu> wrote:

> 1) When is a good time to start building the peptide into the density
> (should I wait until Rfactors improve significantly)?

I would advise waiting until the rest of the model is as good as possible.
That way you can use the difference map as a paper figure without needing
to do any extra refinement to remove model bias later.

2) If so, should I be masking the peptide density somehow so that further
> refinement doesn't flatten out that density?

Further refinement is probably going to make the density clearer, if it's
at full (or near-full) occupancy.

> 3) What is a general good strategy for lowering Rfactors? (Esp if the gap
> between Rwork and Rfree is high..like 28/40 or so)?

Several things to try:
- much longer refinement, say 10 macro-cycles instead of 3 (and even more
may be helpful)
- simulated annealing - although this sometimes has a tendency to overfit,
but right now that's not as big a problem
- weight optimization will reduce the gap between R-free and R-work,
although it will also slow down convergence

But you should also try to make the model as complete as possible -
AutoBuild usually leaves out some residues, and rebuilding them should
reduce your R-factors by quite a bit.  You may be able to simply copy over
appropriate pieces of the original model if they fit the map well (or can
be adjusted easily).

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