Re: [ccp4bb] resolution & R-free

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Neutron Diffraction Instrument Scientist
From: Leighton Coates coatesl {- at -} SNS {- dot -} GOV
Date: 2008-01-03

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Subject: Re: resolution & R-free -- addenda
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2008-01-03

Subject: Re: resolution & R-free
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2008-01-03

Hi Liuquing,

> For example,first,the resolution is 2.25,R-free is 30,completeness is 90%.
> Then I changed resolution to 2.35,R-free became 28.0,completeness is 91%.
> When I changed resolution to 2.45,R-free became 27.5,completeness is 92%.
> So,when resolution from 2.25 to 2.35,R-free goes down a lot,but
> resolution from 2.35 to 2.45,R-free nearly the same,is that meaning
> resolution should around 2.35?

This is pretty expected. Just plot R-factor vs resolution for some good
amount of structures from PDB.

> Should I change resolution during refinement?

Only if you have a very *good* reason for doing so.

> And is there any good software for refinement?
>

Here are few hints of what's out there:

1) SHELXL (great for refinement at high resolution, comprehensive H
atoms handling, twinning; slow since does not use FFT, poor bulk solvent
model, no ML targtes);

2) CNS (uses simulated annealing = large convergence radius; good bulk
solvent model, twinning, uses various ML targets; high-resolution
refinement is not supported, no TLS);

3) REFMAC (TLS, high-resolution refinement, uses ML targets; bulk
solvent modeling often unstable);

4) PHENIX (refinement at any resolution is supported: from ultra-high (<
0.9A) to low with sophisticated rigid body refinement (very big
convergence radius); robust TLS (never gets "unstable"), robust bulk
solvent model (always finds best parameters), simulated annealing, twin
refinement, H handing, alternative conformations; torsion angles
dynamics is not yet implemented).

To find out more about each option -- do Google search.

Cheers,
Pavel.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Neutron Diffraction Instrument Scientist
From: Leighton Coates coatesl {- at -} SNS {- dot -} GOV
Date: 2008-01-03

Next message:
Subject: Re: resolution & R-free -- addenda
From: Pavel Afonine pafonine {- at -} LBL {- dot -} GOV
Date: 2008-01-03