[phenixbb] ramachandran_restraints

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Dec 28 06:32:02 PST 2010

Hi Jose,

Is it possible that the density is inaccurate enough that the "forced out
of density" peptide bonds might actually be closer to the correct
positions than where they were previously?  At resolutions in this range
if the overall ADP's are high and the map is not that clear sometimes
moving things out of density but into geometrically likely configurations
could possibly make the model better.

All the best,
Tom T

>> Dear all,
>> I am refining a structure to 2.9 A, with pretty bad experimental data (P1,
>> ~5400 residues in the A.U. (4 mol), anisotropic, fairly incomplete...). I
>> have been running phenix.refine with NCS, 1 ADP per residue, lower target
>> weights, TLS. My R/Rfree are stuck at about 2.4/3.05. I was getting around
>> 2% ramachandran outliers at every cycle so I have been giving the nightly
>> builds a shot. Now I get 0.2% outliers without changing any parameters for
>> the ramachandra_restraints but it is forcing some of the peptide bonds out
>> of the density. What can I tweak to improve the refinement?
>> Thanks all in advance!
>> Jose
>> José Trincão, PhD	CQFB at FCT-UNL
>> 2829-516 Caparica, Portugal
>> "It's very hard to make predictions... especially about the future" -
>> Niels Bohr
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