On Oct 14, 2010, at 2:28 PM, Jacob Keller wrote:
> I have always found this angle independence difficult. Why, if the anomalous
> scattering is truly angle-independent, don't we just put the detector at 90
> or 180deg and solve the HA substructure by Patterson or direct methods using
> the pure
On Oct 14, 2010, at 2:31 PM, Tim Gruene wrote:
> I would like to understand how the notion of a photon being scattered from all
> electrons in the crystal lattice explains the observation that radiation
> damage
> is localised to the size of the beam so that we can move the crystal along and
> sh
It is mostly because in the higher angles intensity of the reflection is lower,
precision is lower and anomalous signal is washed out by counting statistics.
For very well diffracting test crystals anomalous signal is MEASURABLE to very
high resolution providing good enough I/sigma(I) is generate
On Thursday, October 14, 2010 02:28:26 pm Jacob Keller wrote:
> I have always found this angle independence difficult. Why, if the anomalous
> scattering is truly angle-independent, don't we just put the detector at 90
> or 180deg and solve the HA substructure by Patterson or direct methods using
On Thu, 2010-10-14 at 23:31 +0200, Tim Gruene wrote:
> you observe that each photon decides on exactly one slit
> that it goes through.
That is if you observe which slit it goes through.
--
"I'd jump in myself, if I weren't so good at whistling."
Julian, King of L
On Thu, 2010-10-14 at 23:31 +0200, Tim Gruene wrote:
> I would like to understand how the notion of a photon being scattered
> from all
> electrons in the crystal lattice explains the observation that
> radiation damage
> is localised to the size of the beam so that we can move the crystal
> along
On Thu, Oct 14, 2010 at 04:28:26PM -0500, Jacob Keller wrote:
> I have always found this angle independence difficult. Why, if the anomalous
> scattering is truly angle-independent, don't we just put the detector at 90
> or 180deg and solve the HA substructure by Patterson or direct methods using
Good evening citizens and non-citizens,
On Thu, Oct 14, 2010 at 08:21:19AM -0700, William G. Scott wrote:
> On Oct 14, 2010, at 7:40 AM, Ed Pozharski wrote:
>
> > On Thu, 2010-10-14 at 08:41 +0200, Tim Gruene wrote:
> >> This sounds as though you are saying that a single photon interacts
> >> wit
I have always found this angle independence difficult. Why, if the anomalous
scattering is truly angle-independent, don't we just put the detector at 90 or
180deg and solve the HA substructure by Patterson or direct methods using the
pure anomalous scattering intensities? Or why don't we see pur
Hi Ed
refmac 5.6 should not have this problem. Yes, you are right. It should be
considered as a bug.
I think I have fixed it. Could you please try 5.6version from:
www.ysbl.york.ac.uk/refmac/latest_refmac.html
You need to take experimental version (it should be stable enough, although I
upda
It appears that external restraints are included in bond_rmsd
calculation. When they are used to restrain the hydrogen bonds to
maintain the Watson-Crick pairing in a 3A resolution structure of a
protein-DNA complex, the bond_rmsd is inflated about 5 times. To verify
this, the refmac run was done
On Thursday, October 14, 2010 01:18:04 pm Bart Hazes wrote:
>
> On 10-10-14 01:34 PM, Ethan Merritt wrote:
>
>
> ...
>
> The contribution from normal scattering, f0, is strong at low resolution
> but becomes weaker as the scattering angle increases.
> The contribution from anomalous scatte
Faculty Position
Department of Molecular Biology
Princeton University
The Department of Molecular Biology at Princeton University invites
applications for a tenure-track faculty position at the assistant
professor level. We are seeking an outstanding investigator in the area
of biochemistry a
On 10-10-14 01:34 PM, Ethan Merritt wrote:
...
The contribution from normal scattering, f0, is strong at low resolution
but becomes weaker as the scattering angle increases.
The contribution from anomalous scattering, f' + f", is constant at
all scattering angles.
...
My simple
Dear Ed,
I think you was "too fast and easy" in your comment.
Tensors are entities that have special rules when changing the coordinate
system.
That's not the case for "any matrix".
Best regards,
Sacha
De : CCP4 bulletin board [ccp...@jiscmail.ac.uk] d
On Thursday, October 14, 2010 12:12:18 pm Lijun Liu wrote:
> I think I need make it clear. Not their changes (f' and f") but their
> contribution to reflection intensities changes.
f' and f" are not "changes".
They are the real and imaginary components of anomalous scattering.
They are wavele
On Thursday, October 14, 2010 10:41:17 am Lijun Liu wrote:
> Power on scattering by atoms is angle dependent, which is true for
> both the real and imaginary parts.
Actually, no. The f' and f" terms are independent of scattering angle,
at least to first approximation. This is why the signal fr
On Oct 14, 2010, at 7:40 AM, Ed Pozharski wrote:
> On Thu, 2010-10-14 at 08:41 +0200, Tim Gruene wrote:
>> This sounds as though you are saying that a single photon interacts
>> with several
>> electrons to give rise to a reflection.
>
> Not only with several - it shouldn't be much of an exagger
Is there anybody out there who has a use for these glasses/emitters that
would be willing to purchase some for a reduced fee? I have 16 pair (I
think, I need to go check closely, but I have a lot of them), plus 6-7
emitters. I just need to go away from this type of system, probably to
a mixed
Power on scattering by atoms is angle dependent, which is true for
both the real and imaginary parts.
(Think about the plot of f vs sin(theta)/lamda).
The f" contribution to anomalous scattering of F(000) is 0, just in
contrast to that the real part in this (000)
direction is the full number o
On Thu, 2010-10-14 at 09:11 -0700, James Holton wrote:
> I wonder if anyone on this
> thread can explain to me the difference between a matrix and a
> tensor?
Matrix is a 2nd order tensor. Tensors may have any number of
dimensions, including zero. Tensor is just a fancy name for a
multidimensi
As I sit here listening to the giant "whoosh" sound of all the world's
biologists unsubscribing from the CCP4BB, I wonder if anyone on this
thread can explain to me the difference between a matrix and a tensor?
Since when are there biologists on this bb?
JPK
p.s. Is "whooshing" biologist-spec
Dear colleagues,
I would like to draw your attention to an upcoming webinar to be presented
by Bernhard Rupp titled "Scientific inquiry, inference and critical
reasoning in the macromolecular crystallography curriculum". In this
webinar, Bernhard will expand on his recent Journal of Applied
Cr
yes there is a F000, it is always in diffraction condition independent
of crystal orientation (hx+ky+lz) is always zero for any xyz when hkl = 000
There are no Miller planes but I guess you can think of a "Miller volume"
F000 is normally not use in map calculations and that is why the average
va
On Thursday, October 14, 2010 09:11:50 am James Holton wrote:
> As I sit here listening to the giant "whoosh" sound of all the world's
> biologists unsubscribing from the CCP4BB, I wonder if anyone on this
> thread can explain to me the difference between a matrix and a tensor?
In invoking the l
Following feedback from students, collaborators and other structural
biologists, the Protein Data Bank in Europe (PDBe; pdbe.org) has become aware
of a need for a social networking presence to strengthen the link with current
and potential users of its resources.
So if you would like to be
This F000 reflection is hard for me to understand:
-Is there a F-0-0-0 reflection as well, whose anomalous signal would have a
phase shift of opposite sign?
-Is F000 always in the diffraction condition?
-Is there interference between the scattered photons in F000?
-Does F000 change in amplitude
Two ideas:
1. Create a file in your home directory called ~/.curlrc
and in it put the following line:
-P - ftp
2. Use wget
first, install wget with fink
Then put the line
DownloadMethod: wget
into the file
/sw/etc/fink.conf (or /sw64/etc/fink.conf ).
I use wget. It seems to be mor
Just to throw a monkey wrench in here (and not really relevant to
the original question)...
I've understood that, just as the real part of F(000) is the sum
of all the "normal" scattering in the unit cell, the imaginary part
is the sum of all the anomalous scattering. This means that in the
As I sit here listening to the giant "whoosh" sound of all the world's
biologists unsubscribing from the CCP4BB, I wonder if anyone on this
thread can explain to me the difference between a matrix and a tensor?
I ask because I think stress and strain are mechanisms of radiation
damage, but whe
Ed,
I think you're confusing 'electric current' with 'electric current
density'. The first is a scalar, the second a vector. The current I
is defined as the surface integral of the density vector J with
respect to the element of area dA:
I = integral over S (J.dA) (how I wish we could use pro
Ed,
The direction of current in an electrical circuit has nothing to do
with any coordinate system. It is defined by convention in electricity
as the direction opposite to that in which the electrons are moving. So
the current is indicated as being from + to - in a circuit. Of course,
you may chan
Again, definitions are a matter of choice. Under your strict version I
still may consider electric current as vector, if I introduce the
coordinate system in the circuit. When I transform the coordinate
system (from clockwise to counterclockwise), current changes direction
with it. By the way, c
Electrical current is a 4-vector, is it not?
> Correct! - and an alternating electric current is represented as a
> complex number (then it's conventional to use the symbol 'j' for
> sqrt(-1) to avoid confusion with 'i', the symbol for electric
> current!). Since as you say electric current is a
Correct! - and an alternating electric current is represented as a
complex number (then it's conventional to use the symbol 'j' for
sqrt(-1) to avoid confusion with 'i', the symbol for electric
current!). Since as you say electric current is a scalar not a
vector, then a complex number has to be a
> The definition game is on! :)
>
> Vectors are supposed to have direction and amplitude, unlike scalars.
I think that this is part of the problem here. Whilst vector quantities do
possess both size and direction, not everything that possesses size and
direction is necessarily a vector by definiti
The definition of a vector as being something that has 'magnitude' and
'direction' is actually incorrect. If that were to be the case, a
quantity like electric current would be a vector and not a scalar.
Electric current is a scalar.
A vector is something that transforms like the coordinate system
On Thu, 2010-10-14 at 08:41 +0200, Tim Gruene wrote:
> This sounds as though you are saying that a single photon interacts
> with several
> electrons to give rise to a reflection.
Not only with several - it shouldn't be much of an exaggeration to say
that the photon senses all the electrons in th
The definition game is on! :)
Vectors are supposed to have direction and amplitude, unlike scalars.
Curiously, one can take a position that real numbers are vectors too, if
you consider negative and positive numbers having opposite directions
(and thus subtraction is simply a case of addition of a
I don't see any conflict here: all you're saying is that there's a
1-to-1 mapping between the complex scalar a+i*b in C and the 2-D
vector (a,b) in R^2.
However the vector does not have all the properties of the original
complex scalar: for example I can happily compute a value for
log(a+i*b) but
Dear Mads,
the first error message _might_ be due to a dead link, but without further
information that's difficult to tell.
The second error message says that curl tried to get the archive using ftp. When
you download something through the ccp4 web site your computer is probably using
http, and m
On Thu, Oct 14, 2010 at 12:34:30PM +0100, Ian Tickle wrote:
> Formally, a complex number (e.g. a structure factor) is not a vector.
Formally, C is isomorphous to R^2 (at least that's what math departments in
Germany teach, and it's not difficult to prove), therefore complex numbers are
vectors. Tha
Formally, a complex number (e.g. a structure factor) is not a vector.
Just because the addition & subtraction rules (i.e. 'a+b' & 'a-b') are
defined for real numbers, complex numbers and vectors doesn't make a
complex number a vector, any more than it makes a real number a vector
(or vice versa).
I have a problem installing CCP4 on a MacOSX 10.6.4.
When I follow the procedure on Bill Scott's web-pages to install the
precompiled version, I get an error message saying
Err http://sage.ucsc.edu stable/main Packages
403 Forbidden
When trying to install it via the normal Fink way, I get
curl
To try to answer the Q I think you are asking..
If you keep anomalous seperate you will get a file from ctruncate with h
k l F+ SIGF+ F- SIGF- I+ SIGI+ I- SIGI-
The observations flagged as F- or I- etc are actually measured for the
reflection -h-k-l
So uniqueify generates markers for eac
Dear Colleagues,
I see I should quote the last sentence of our abstract of Bradbrook et al 1998:-
This work demonstrates the difficulty in relating structure to
thermodynamics, but suggests that dynamic models are needed to provide
a more complete picture of ligand - receptor interactions.
Be
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