Dear all,
We extended the registration to the course for a week. You are kindly
invited to register. Share this information with people that might be
interested.
The Biocenter Finland Protein crystallisation unit is organising an
advanced workshop in protein expression, characterisation an
Sir one more help plz i have the following matrix which one shall i use to
calculate the angle.
INFO:: coordinates transformed by orthonal matrix:
| -0.6927, -0.7191,0.0564|
| -0.4828,0.5204,0.7043|
| -0.5358,0.4606, -0.7076|
( 76.04,-10.19, 28.64)
Rotation
We have two open positions in the Structural Biology Department at Genentech.
Please submit applications to http://www.gene.com/careers quoting the
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Job Description
Position available for a Research Associate/Senior Research Associate to
My real questions is:
Does d*trek recognize the img file format collected at ALS or APS and
process the data?
Thanks!
On Thu, Aug 23, 2012 at 6:00 PM, jlliu liu wrote:
> Do anybody know if d*trek can process data collected from APS? Thanks a
> lot in advance.
Do anybody know if d*trek can process data collected from APS? Thanks a
lot in advance.
Glad to clarify!
Also, note that whilst the "springs between atoms" analogy is nice for
visualisation purposes, and certainly helps to initially explain the concept,
it is not technically correct. Certainly, a similar analogy would be
appropriate for external restraints and NCS local restraints
Dear Appu,
I had similar issue once. You can use Coot to overlay two structures and
get the rotation matrix
a1 a2 a3
b1 b2 b3
c1 c2 c3
from here you can calculate cosine of an angle using formula
(a1+b2+c3-1)/2
Good luck,
Nikolina Sekulic, PhD
postdoctoral fellow
University of Pennsylvania
O
Hi Roger,
You are correct, that *conceptually* the contribution to the target function is
sum(w (|d|-|dcurrent|)^2)… however this is not actually applied to the target
function. The target function remains unchanged. Only the 2nd derivative is
affected by the jelly-body restraints.
Also, note
Garib gave a nice description of jelly-body refinement at the ACA
meeting. IIRC from his talk, conceptually jelly-body refinment is the
equivalent of adding "springs" between atoms within a certain radius of
each other that restrain their movement during refinement. The
restraints contribute to
Dear all ccp4 users,
I have solved the structure of a protein
which is a dimer. On comparison with the other structure from PDB data
bank, i found that structure solved by us show a tiltness in
monomer-monomer arrangement of a dimer. May you please help me in findn
I figured it out
ATOM 48 C PRO A 11 59.322 -42.497 -19.375 1.00
39.11 C
ATOM 49 O PRO A 11 58.425 -42.192 -20.159 1.00
36.42 O
HETATM 50 N NH2 A 11 60.520 -42.416 -19.709 1.00
46.31 O
TER
-- Forwarded message -
Oh, I thought the sigmas were derived from the differences in intensities
of the multiple measurements of a given reflection--I guess both the
individual-measurement counting stats and differences in measurements must
be combined in the end. But, what does the software do if somehow a sigma=0
creep
On Thu, Aug 23, 2012 at 10:44 AM, Jim Pflugrath
wrote:
> Singly-measured reflections should have a sigma from Poisson counting
> statistics, so that should not be a problem. A problem might occur if the
> X-ray background is exactly zero and the observed (sic) intensity is exactly
> zero.
Or the
Oops, I meant if the variance of the X-ray background is exactly zero (and not
if the X-ray background is zero). Think about that in the context of Poisson
counting statistics. :)
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jim Pflugrath
[jim
Hi Nathan,
Jelly body refinement is basically a way of stabilising refinement, helping to
achieve a more robust estimate of the curvature of the likelihood function,
thus leading to a more robust search direction. This is similar to other
regularisers used in refinement, e.g. geometry restraint
Singly-measured reflections should have a sigma from Poisson counting
statistics, so that should not be a problem. A problem might occur if the
X-ray background is exactly zero and the observed (sic) intensity is exactly
zero.
From: CCP4 bulletin board [CCP4BB
Dear experts,
Could someone explain what it is exactly that jelly body refinement
does? I think that I understand it intuitively but want to make sure.
In the same vein, what does jelly body refinement sigma parameter
control? I.e., in comparison to the default sigma = 0.02, does sigma =
0.1 make
How would I tell REFMAC to replace the
C-terminal Pro in my synthetic peptide
with a CONH2
not
the natural CT.
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