Dear James,
what an interesting discussion!
Am 30.01.2009 um 19:42 schrieb James Holton:
...
I think the coherence length is related to how TWO different photons
can interfere with each other, and this is a rare event indeed. It
has nothing to do with x-ray diffraction as we know it. No
Thanks Colin,
Yours is one of several lessons I have received on coherence and optics
in the past few days. I do appreciate all effort and the input.
However, as I mentioned before I am a biologist and I don't so much care
about the fundamental nature of the universe as I do about how it
Hello -
Sorry if some of my suggestions are redundant since I jumped in late
in this thread.
A couple of additional comments after struggling with a similar albeit
not identical case.
With a pseudo translation vector like that the SG could be any of
the 8
orthorhombic SGs; P222 P21 22
We have seen that the recent versions of phenix (1.3) the structure
refinement ends with a bulk solvent correction step, something I found
quite unusual (absent in other refinement programs and in older versions
of phenix, 1.24.1). We have also seen that the B factor jumps up in
this last step
Chi2 is unusually high at lower resolution (Chi2 is 3 from 3.5A as
shown
below) and there is a relatively high percentage of rejections (1.5 %).
Chi^2 in Scalepack *must* be adjusted by changing the expected errors to be
about 1.
Until then, I would not reject reflections. Only
Dear All,
I have a 9-kDa protein that crystallizes well. Since there is no structural
homologue for this molecule, I intend to make Se-Met derivative of the
protein. The molecule has no Met/Cys residues in its sequence. I wanted to
know where in the sequence should I mutate, so that the
Hey Amit,
as your protein is tiny, maybe you can calculate a molecular replacement
model as described in Acta Cryst. (2009). D65, 169–175.
This might take longer than engineering a few methionines, though. I'd
mutate leucines.
Andreas
amit sharma wrote:
Dear All,
I have a 9-kDa
Re my previous post of this title:
Harry Greenblatt just pointed out that I should have said that it is the
reciprocal cell edges a* and b* that are non-equivalent in P4, not the
real-space cell edges a and b. Hope that didn't confuse too many people.
-James Holton
MAD Scientist
Hi Jose,
We have seen that the recent versions of phenix (1.3) the structure
refinement ends with a bulk solvent correction step, something I found
quite unusual (absent in other refinement programs and in older
versions of phenix, 1.24.1).
- the software is evolving and gets better over
I have trouble with visualizing things in three dimensions so I'm
trying to figure out the relationship between two cross rotation
functions (given as theta1, theta2, theta3).
Is there a program or webapp that'll tell me whether two rotation
solutions are related by a
Hi Amit,
Based on the original analysis of M. Dayhoff (PAM matrix, Dayhoff
substitution probability, Dayhoff, et. al 1978), introduction of Leu-Met would
be the best choice for production of Se-Met derivatized protein.
It would be best to consider a multiple sequence alignment of
A two-day workshop focused on both the basics and the current
development in macromolecular
single crystal structure refinement techniques will be held in Prague on
April 3-4 2009.
The workshop is organized within the TeachSG project of the EC (tightly
connected with the project
I forgot to mention that I think the only fail-safe direct approach
will involve converting both rotations into quaternions,
subtracting (inv(A)*B) said quaternions, then converting the
difference into an axis-angle pair.
James
On Feb 3, 2009, at 9:47 AM, Francis E Reyes wrote:
I have
Dear colleagues,
I have just deposited an entry on the ccp4-wiki that summarizes input/ideas
on dealing with 'sticky crystals'. Please feel free to edit it further as
necessary.
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Crystals#Crystal
_handling
best wishes
Savvas
Hello,
After installation I tried Graphical View of Project and I got:
dotgraph_render: error: graph 1.000 5.861 0.528
node Job1 0.472 0.264 0.945 0.500 1: autoSHARP\nautoSHARP filled box
black #9DD05B
node Job2 1.667 0.264 0.945 0.500 2: autoSHARP\nautoSHARP filled box
black #9DD05B
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