Dear All,
I want to thank all for your helpful and quick suggestions and insight.
It was a very good discussion and also helped in understanding the topic.
Thanks again.
--
Sonali Dhindwal
“Live as if you were to die tomorrow. Learn as if you were to live forever.”
--- On Mon, 18/3/13, Ian T
Hi all,
I am refining a structure of protein-DNA complex with coot. The DNA in
my search model is shorter than the DNA in the crystal, and now I
could see the density for extra DNA(6 base pairs) on either end of the
search model DNA. But, I don't know how to build the extra DNA back to
fit the dens
Dear all
What is the right (cost wise) purity level for DNA oligonucleotide synthesized
for cloning, site-directed mutagenesis and protein/DNA co-crystallisation?
Thank you.
Theresa
On 17 March 2013 13:19, Robbie Joosten wrote:
Small addition to Ian's comment. The value you give with 'weight auto
$value' is a starting value. Refmac will gradually change it if needed
(it's autoweighting after all) and your starting value does matter
somewhat. Based on Ian's advice PDB_REDO use
On Sunday, 17 March 2013, Pavel Afonine wrote:
> Hi Ethan,
>
>
> I would place the expected resolution break-even point at more like
> > 1.2 - 1.3 A. But that's only an expectation, not a rule to rely on.
> > You should justify anisotropic refinement of a structure on the basis
> > of its own pa
Hi Ethan,
I would place the expected resolution break-even point at more like
> 1.2 - 1.3 A. But that's only an expectation, not a rule to rely on.
> You should justify anisotropic refinement of a structure on the basis
> of its own particular model and measured data. Robbie Joosten has
> alrea
On Sunday, 17 March 2013, Pavel Afonine wrote:
> Hi Sonali,
>
> regarding isotropic vs anisotropic parameterization of your individual
> ADPs: apart from common sense and theoretical considerations, this is also
> in great part software dependent.
>
> I can't speak for other programs, but for phe
Hi Sonali,
regarding isotropic vs anisotropic parameterization of your individual
ADPs: apart from common sense and theoretical considerations, this is also
in great part software dependent.
I can't speak for other programs, but for phenix.refine I would say the
rule of thumb is:
- higher than 1.
Dear Dr Zhu,
I hope the following might make things easier to grasp. The 3.0Angstrom
diffraction resolution is basically required to resolve a protein polypeptide
chain whether your protein is in an 80% solvent content unit cell or a 50%
solvent content unit cell. You will have more observations
One issue is whether the extra data for the 80% solvent volume consists of
independent measurements. The references below suggest that the required
"oversampling " of intensities is given when one has a 50% solvent volume.
J. Miao, D. Sayre, and H. N. Chapman, "Phase retrieval from the magnitud
Hello,
I have been using this portal for past eight years, learned many intricate
aspects of crystallography. now that I have changed my career please make
sure to remove me from the list.
I wish you all wonderful years and best wishes.
Sincerely,
Santosh
Small addition to Ian's comment. The value you give with 'weight auto $value'
is a starting value. Refmac will gradually change it if needed (it's
autoweighting after all) and your starting value does matter somewhat. Based on
Ian's advice PDB_REDO uses a starting value of 2.50 which seems to do
Hi Sonali
The 'WEIGHT MATRIX Wm' scale factor, to which I assume you're referring, is
on a relative, not absolute, scale so is not comparable between different
models, i.e. the results will be substantially different when you change
the model keeping Wm fixed as you discovered. If you want the we
Wonderful, thanks very much to all the CCP4 team !
[ I have met users who object to "command lines" and "terminals" and
"no-clicking", for them if it's not in the GUI it's "yuk" but I guess
that you can't have everything :-) ]
Fred.
On 16/03/13 22:16, andrey.lebe...@stfc.ac.uk wrote:
After
Dear Sonali,
There is no such thing as an ideal rmsd for bonds and angles given resolution.
IMO you should use rmsZ which also doesn't have an ideal value. If its below 1
your good. As for the isotropic vs anisotropic, you can use a hamilton test if
you do two refinements changing only the B-fa
Dear James,
I agree with your chronology of the first full new protein structures by SR
MAD.
The 1975 two wavelength Hoppe and Jakubowksi study of erythrocruorin with Ni
and Co Kalpha Xray tubes is a classic piece of work of in effect MAD phasing .
See the IUCr Anomalous Scattering Conference
Dear All,
We want little suggestion and knowledge regarding refinement of data in Refmac.
We have a data with resolution upto 1.5A. Overall redundancy of 5.5 and 3.7 in
high resolution bin. and I over Sigma is also 21 overall and 2.2 in last
resolution bin.
When we first did isotropic refinem
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