FreeR flags are a bit of a pain - there is the number you should select,
then how to compensate for non-crystallographic symmetry and putative
twinning.
Vilmos has written a useful Rfree assignment tool which covers possible
twinning problems. It selects FreeR flags for the highest Laue symmetry
I’ll also add for completeness, that (in Phenix at least) by default a total of
2000 reflections will be selected at most - meaning if you have a lot of
reflections the total percentage selected will be substantially less than 10%
or even 5%.
> On Jul 10, 2018, at 7:44 AM, Pavel Afonine
It's important to remember that free-R reflections are not only used to
calculate Rfree, but also are used in calculation of m and D scales in
2mFo-DFc and mFo-DFc maps, as well as in likelihood-based refinement
targets. The fact is that you need to have a sufficient amount of free-R
reflections
Dear Colleagues,
let me draw your attention to the ECM31 Satellite Meeting:
"Progress in instrumentation for X-ray diffraction and CryoEM"
https://ecm31.ecanews.org/en/progress-instrumentation-x-ray-diffraction-and-cryoem.php
This satellite meeting will present an overview of a wide range of
Dear all we are pleased to announce a 1 day structural biology symposium at
Diamond covering exciting research and topics in MX, CryoEM, XFELs and MicroED
on the 16th August. The symposium is a unique opportunity for UK structural
biologists to learn more about structural biology research and
On 10/07/2018 09:32, Grandi, E. wrote:
Dear all,
Hello Eleanora,
I am recently working on a protein-ligand structure. The problem is that the ligand is not present in the
library used by Refmac. Therefore, after having modified the structure on Coot I cannot run Refmac again
because the
Dear Shijun,
For refinement you want to use as much good data as possible to get a good
model. At the same time you want to make sure that your model is predictive for
related data that was not used for making that model. This wat they call
holdout validation and that is exactly the idea
Dear all,
I am recently working on a protein-ligand structure. The problem is that
the ligand is not present in the library used by Refmac. Therefore, after
having modified the structure on Coot I cannot run Refmac again because the
ligand is not recognized. The program suggest me to use JLigand
The precision or significance of rfree depends on the number of reflections
used to calculate it. No fixed rule for percentage exists. Tickle & Brunger
have elaborated on this. References pp 625 in bmc. Depending on how many
data overall you have and can set aside, for an overall rfree uncertainty
Dear all
I am confusing the choose of free R-flags recently. Rfactor means calculatted
from reflection not used in refinement,so what's big the difference between
different percentage of R-flags,like it's about 5% in ccp4 -refmac, while it is
10% in phenix-refinement,what's the difference
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