Dear Sampath,
You are right, the gap between R and Rfree is significant and indicates that
your model was overfitted.
Without knowing your data or your model, some reasons for overfitting might be:
- you used automated placement of water molecules (e.g. through arpwaters or in
coot) and never ch
Hi Sampath,
this is how the distribution of Rwork, Rfree and Rfree-Rwork look like
for 'all' PDB structures refined at around 2A resolution. The "<<<"
indicates where your structure stands with respect to this distribution.
Histogram of Rwork for models in PDB at resolution 1.90-2.10 A:
0
Dear all,
I have a question about the R free value. I refined a structure with 2A
resolution. After model building and restraint refinement using Refmac
program, the average B factor was around 50 for all atoms. The R/Rfree were
around 22/34. Then used the TLS refinement choosing entire molecule.
Traditionally, the Protein Data Bank (PDB) has been accessed mostly by PDB
accession code, or by searches based on information regarding, for instance, a
publication, a molecule name, a sequence or a related 3D structure. While
these methods are valuable for locating a specific PDB entry or grou
Hi,
I want to calculate the portion of the "noise" density with respect to the
whole unit cell (assuming the model is good enough). I plan to first
calculate the integral density within the whole unit cell, then build a
atom mask around the molecule and calculate the integral density within
the ma
The "rule" is that the average isotropic temperature factor for your protein
atoms should not differ too wildly from the Wilson B-factor of the data set
(when you convert your anisotropic B's to isotropic B's). Otherwise there is no
such thing as an acceptable or unacceptable value, the value is
Dear Anja,
I'm not sure why you want the orientation of the
molecule in pymol, but working out the orientation of the crystal at
phi=0 is straightforward in imosflm.
Read the image, index it and go to Strategy". In the strategy pane it
gives the angles between the a,b,c a
HI ALL,
Thanks Dirk and Pavel for clearing up the discrepancy between the R values
going from Refmac5 to SF-check. On the same note, i have a large anisotropic B
factor( atomic model) once I carry out the TLSANL process. Is there an
acceptable value for this?
cheers
rakesh
Dear Anja,
every integration software determines and most likely also prints the
orientation matrix of the crystal's unit cell w.r.t. the laboratory coordinate
system. With XDS, this matrix can be found in GXPARM.XDS, with mosflm you
entered that matrix' name when you refined the cell parameters.
Hi there,
we were taking UV/ vis spectra of a protein crystal that show
different features depending on the crystal orientation in the beam.
The question is now how to correlate the UV/ vis spectra with the solved
structure. We know that it has a special feature at e.g. image 1 (0°). So
how can we
Dear Engin:
I've put placeholder packages for those entitled "imosflm-aqua" and "mosflm" in
fink CVS that simply point back to what is in ccp4. The "imosflm" package
remains a placeholder with dependencies on all the X11-based tcl/tk extensions
required to get imosflm in ccp4 to work with an X
The Institute of Cancer Research
(University of London)
Section of Structural Biology
Chelsea, London
Post-doctoral Training Fellow
Structural Biology of proteins involved in DNA replication and repair
The Institute of Cancer Research (a College of the University of London) is
a world-class c
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