regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
On 3/19/20 06:00
,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
On 1/21/20 12:55, Chris
r 19.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/pe
g or model building.
Also, ContaMiner seems to be a great resource:
https://strube.cbrc.kaust.edu.sa/contaminer/submit
Best wishes,
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jeff
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
On 8/2
Pavel,
Sorry for an unclear sentence. What I meant was:
My conclusion is that "no fill-in" option might be tried at some stages
for datasets with low high res completeness. But, if a dataset ALSO has
low completeness in low-medium shells, then extra caution should be
applied. In my case,
t maps looked
somewhat better, as I wrote before.
My conclusion is that "no fill-in" option might be tried at some
stages, but with caution, especially for datasets with poor low res
completeness.
Many thanks to everyone!
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scien
Pavel,
Thanks for pointing that out.
Based on one dataset, it seems to me that using this kind of maps
"no-fill" as an additional guide can help tracing some side-chains.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and
Dear Clemens,
Thanks!
It sounds like a good test to do on the output .mtz and see if there are
any significant changes in maps after these "filled in" coefficients are
removed.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular
ement"
Thanks!
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.
,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://www.linkedin.com/in/shabalinig/
https://minorlab.org/person/ivan_s/
On 8/3/19 05:03, Robbie
that is too low to include it in
Table 1?
Many thanks,
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
https://ww
, the deposition to the PDB goes first, and the
deposition of images goes second.
Thanks,
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA
so, especially because
depositing images is very easy these days with services like SbGrid,
proteindiffraction.org (also known as IRRMC), and Zenodo.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University
to do, as pointed by others), it
in not clear to me why not to extend. And Rfree of 36% seems really high.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room
izing metal-binding sites in proteins with X-ray crystallography"
https://www.ncbi.nlm.nih.gov/pubmed/29674755
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall
atoms.
If the dataset is very good, and the wavelength of X-ray is rather long,
you might even get anomalous signal for Ca:
http://skuld.bmsc.washington.edu/scatter/AS_periodic.html
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology
ratio stands for
"data-to-parameter ratio" = 2 or higher. One atom is defined by 9
parameters.
2) Drop of R-free has to be meaningful (significant). My rule of thumb
is that at least 0.5% percent is good. 1% is safer.
Ivan
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
On 12/14/2017 07:08 AM, Jiyong Su wrote:
Dear CCP4bb,
In 2014, I collected a high
artifacts much easier, and save much effort for those who are new (or
not very new!) to such cases.
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223
lds to see if there are diffraction spots at all.
Good luck!
With best regards,
Ivan Shabalin, Ph.D.
Research Scientist,
Department of Molecular Physiology and Biological Physics,
University of Virginia,
1340 Jefferson Park Avenue, Pinn Hall,Room 4223,
Charlottesville, VA 22908
X-ray weight is low?
And what does mean, that for Mg there is no standard deviation of the bonds (.
# ? is placed instead)? How phenix will handle it? will it assign some default
esd?
I appreciate any comments! Thanks a lot!!
With best regards,
Ivan Shabalin, Ph.D.
Research Associate
Im very grateful to the community for supporting me with so interesting
information!
Now my understanding of the subject is much better!
With best regards,
Ivan Shabalin
with significant decrease in atom size (that can have the same effect as Bf
lowering)? With Bf=0 the difference in curves is significant.
With best regards,
Ivan Shabalin
Does that mean, that with Bf10 we cannot distinguish Mg and water by electron
density peak profile? Even if oxygen in water has twice as much bigger radius
than Mg2+? I have one more question about modelling ions and im going to ask it
in a separate post.
Thanks a lot!!
With best regards,
Ivan
it really make significant
difference for refining?
2) Is it possible to specify atom type in the library, so that the scattering
factor coefficients will be taken into account by Refmac? Or changing PDB-file
manually is the only way?
Thank you very much for any comments!!
With best regards,
Ivan
not to change scattering factor at
all.
Thank you very much!!
With best regards,
Ivan Shabalin, Ph.D.
Research Associate, University of Virginia
4-224 Jordan Hall, 1340 Jefferson Park Ave.
Charlottesville, VA 22908
I would just model it with one water. Especially if resolution is worse than
1.8 (I dont think you have better based on the map)
Only if resolution is high and R-factors are low I would worry about this peak.
Regards,
Ivan
Dear all,
I have an atomic resolution (1.1#197;) structure of enzyme with the bound
cofactor NAD. During the analysis of the refined structure I found that
important double C=O bond of the cofactor in the active site was slightly
lengthened from standard 1.22#197; to 1.26#197;. Then I increased
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