If you can calculate the transformation between the 2, the rotation (kappa)
that relates them is found using the formula:
2 cosine (kappa) + 1 = Trace (transformation)
where Trace = sum of diagonal elements.
Doug
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk
We had success substituting an Arg to Met.
It might seem counterintuitive (basic -> hydrophobic), but the
underlying reason was that this Arg was involved in DNA-binding and the
mutant was designed to effectively clip off the guanidino group while
leaving the rest of the sidechain intact.
It
Hi all,
I was trying to install the newest CCP4 on my macbook pro and got this
error message. I could not save anything and create new project.
ERROR unable to make logging file /Users/home/.CCP4/dbclientapi.log
Traceback (most recent call last):
File "/sw/share/xtal/ccp4-6.1.0/share/dbccp4
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
James and other enthusiasts
First of all, to help James with his identity crisis, he is not a biologist or
a physicist. He is a biophysicist. A noble pursuit. It also has the advantage
that you can impress your biology friends with your knowledge of physics and
impress your physics friends with
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
Savvas
Transform a molecule according to the two transformations in which you
are interested and then use dyndom to see the hinge axis that relates
the two transformed molecules.
On Feb 3, 2009, at 9:47 AM, Francis E Reyes wrote:
I have trouble with visualizing things in three dimensions so I'm
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 Spine2-Complexes
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 yo
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 180/90/60/whathaveyo
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 t
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
Hey Dirk,
You're wrong. ;)
Well, actually, it depends on what you mean by "intensity". As Colin
pointed out the word "intensity" is practically useless unless you are
sure that you are comparing "apples to apples". In crystallography, you
get beam intensity in flux (photons/s) but the inte
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 prote
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
folding/c
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
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
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
re
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
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