[phenixbb] low-resolution refinement

[Nathaniel Echols]

On Fri, Jun 10, 2011 at 5:43 PM, Jennifer Weinreich <
jenn.a.weinreich at gmail.com> wrote:

> 2) What is the expected (or 'acceptable') gap between R and Rfree at this
> resolution.  (Current R = 27%, Rfree = 33%)  Does this sound reasonable?
>

It's not unreasonable, but you can probably narrow the gap if you get the
reference model restraints working.  (For comparison, I've spent most of the
last week playing around with low-resolution data, and two of my test cases
are a 3.6A structure with R/R-free = 0.285/0.335, and a 4.0A structure at
0.27/0.34 - both published, and originally refined with Phenix.)

3) It has been suggested to me that I should try adding riding hydrogens
> during the last round of refinement (to help with geometry).  Is this
> something I should do?
> And if so, should I remove them when I deposit the file to the PDB.
> (Hydrogens at 4.5A are probably going to raise a lot of eyebrows...
>

It's worth a try, but in my experience this often just makes it worse.

5) I have been using secondary structure restraints during the refinement,
> which seems to work reasonably well.  I also tried refinement using
> reference model (the structure of the individual components).  But refining
> with reference models seems to result in high RMSD bonds/angles.  Is there
> something I'm missing?
>

For some reason the reference model restraints often have a weird effect on
the automatic weighting.  Try optimizing the x-ray/stereochemistry weighting
with relatively strict limits for RMS(bonds)/RMS(angles) - on the command
line, for instance:

optimize_wxc=True
bonds_rmsd_max=0.01
angles_rmsd_max=1.5

(and in the GUI, it's in the middle of the second tab in the configuration
section.)

-Nat
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