Dear Keitaro
As far as I know different program behave differently. REFMAC by default
replaces structure factors of the excluded reflections with their expected
values (as a first approximation) that is equal to DFc, where D reflects errors
in coordinates. It seems to be a balance between avoid
Dear all,
I'm very interested in this topic.
I have a question about the default behaviors in output reflection
files of each refinement softwares.
Are test set reflections excluded from the columns for calculating
electron density maps?
I found in phenix.refine documentation the option
electron_
Hailiang,
r-free reflections should not participate in refinement, regardless whether
it is real or reciprocal space one, done with machine driven minimizers or
your hands moving atoms in Coot. Period. The issue of correcting the
map appearance for missing data (resolution or completeness) is rele
It does not matter. By fitting manually you are doing manual minimisation. The
same treatment is applied. You are trying to optimise fit of the model into the
electron density.
I did these tests few years back and results were as expected. Independent on
minimisation tools (manual, automatic, pa
Thanks Garib, but my task was not real space refinement (just manual model
building/adjustment). Following is my previous post. Thanks!
"""I am not doing real space refinement. Actually I am only using the
maps for manual model building/adjustments. In this case, if some Rfree
reflections have st
On Mon, May 23, 2011 at 1:17 PM, wrote:
> Thanks Nat! I am not doing real space refinement. Actually I am only using
> the maps for manual model building/adjustments. In this case, if some
> Rfree reflections have strong scattering intensities, removing them may
> lead to featureless density maps
On Monday, May 23, 2011 01:17:45 pm Hailiang Zhang wrote:
> Thanks Nat! I am not doing real space refinement. Actually I am only using
> the maps for manual model building/adjustments. In this case, if some
> Rfree reflections have strong scattering intensities, removing them may
> lead to featurel
It should be remembered that refining in real space is equivalent to refinement
in the reciprocal space (through Parseval's theorem). If you want to do
consistent refinement then you need to use exactly same reflections for free
and working set. If you do not use the same set of reflections for
Thanks Nat! I am not doing real space refinement. Actually I am only using
the maps for manual model building/adjustments. In this case, if some
Rfree reflections have strong scattering intensities, removing them may
lead to featureless density maps. However, if we just leave them in, do
you think
On Mon, May 23, 2011 at 1:02 PM, Hailiang Zhang wrote:
> I have a preliminary question. I understand Rfree reflection sets are
> never used during automatic refinement, but, when generating the real
> space density maps, do we have to exclude Rfree columns? Any references
> will also be greatly a
I meant :when generating the real space density maps, do we have to
exclude Rfree reflections?
> Hi,
>
> I have a preliminary question. I understand Rfree reflection sets are
> never used during automatic refinement, but, when generating the real
> space density maps, do we have to exclude Rfree c
Hi,
I have a preliminary question. I understand Rfree reflection sets are
never used during automatic refinement, but, when generating the real
space density maps, do we have to exclude Rfree columns? Any references
will also be greatly appreciated!
Best Regards, Hailiang
>do not diffract to sufficiently high resolution so as to allow us to read off
>the sequence from the map).
>Since we have access to a lot of pure protein, I wonder if some clever mass
>spec jock would be able to assemble >enough overlapping sequenced fragments so
>as to give complete coverage
This pops up often enough there ought to be a FAQ.
1) The old glasses & emitters from the CRT days are not compatible with
the new glasses and emitters. Move right to question #2.
2)
a) Pick a 1920x1080 monitor from nVidia's list of approved display
devices: (~ $400)
http://www.nvidia.com/ob
We've crystallized a complex of an Fab bound to a protein. We have the
hybridomas from which the Fab was prepared, but no protein sequence for the
antibody. We're trying to plot the easiest course to get the sequence (since
the crystals, alas, do not diffract to sufficiently high resolution so a
Here are a couple of resources that might be useful to characterize
conformational changes between crystal and solution structures.
1. List of PDB structures solved by multiple methods (NMR, X-Ray, EM):
http://www.pdb.org/pdb/statistics/clusterExpMethods.do
2. Structures can be com
You might want to look into the upsalla compressed mask format (it's an
exact representation of a binary mask - compression is handled by just
tracking the start and end points of the stretches).
Pete
Hailiang Zhang wrote:
Hi,
As I understand, the general molecular mask generated by CCP4 (eg
Dear Colleagues
I'm accepting short communications and articles of general interest to
crystallographers working on macromolecular systems for the next issue
of the Computational Crystallography Newsletter. You can see recent
issues at
http://www.phenix-online.org/newsletter/
as well as the word
*Postdoctoral Fellow Position in Macromolecular Structure Determination *
A postdoctoral fellow position is available in the Taylor Structural
Biology Lab in the Department of Pharmacology at Case Western Reserve
University in Cleveland, OH.
Our work focuses on the structure and function of ma
Seema, I agree completely with Eleanor. You need to take a step back
here. When you say that 'Rfree got stuck at 29-30' what makes you so
sure that this isn't the correct Rfree? Who told you that there's a
problem to be solved in the first place?
If you look at our paper (Acta Cryst., 1998. D54
I dont think there is an Rfree problem..
At 2.7A you expect quite a big difference between R and Rfree
Reducing the resolution will a) probably makethe Rfree/R difference
greater, and b) degrade the quality of your maps and model.
Eleanor
On 05/21/2011 02:28 AM, Seema Mittal wrote:
Hi Ethan,
No offense intended, but NMR is not a structure determination method. One
_estimates_ what a structure _might_ look like if such and such
"restrainoconstraints" applied. We always speak of how undetermined our
crystallographic data are, how poor of an estimate is our R/R-free. Shall we
even dis
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