Dear Srinivasan,
Although the Twilight program can only look at deposited PDB entries, the
tips about ligand validation in the paper are very useful. I suggest you
start from there.
You can use EDSTATS in CCP4 to get real-space validation scores. Also look
at the difference map metrics it gives
Dear Srinivasan,
The first thing I would do is to look very carefully at the electron
density maps: Does it look like a bunch of water molecules, or is
continuous density present? Could it be some buffer component (Tris,
Hepes, sulfate, DMSO etc) or the counter ion of your ligand or the
I guess I have known lots of incorrectedly fitted ligands, and am never
sure quite how to be confident they are correct. Your resolution is good,
so one hopes the density is pretty clear?
Common sources of error.
By far the most common is caused by having an incorrect dictionary. Look
very
One final quote that is not in the twilight paper summarizes it nicely:
The scientist must be the judge of his own hypotheses, not the
statistician.
A.F.W. Edwards (1992) in Likelihood - An account of the statistical concept
of likelihood and its application to scientific inference , p. 34.
One final quote that is not in the twilight paper summarizes it nicely:
The scientist must be the judge of his own hypotheses, not the
statistician.
A.F.W. Edwards (1992) in Likelihood - An account of the statistical
concept
of likelihood and its application to scientific inference , p.
Dear Jacob,
You are overinterpreting, the statement is about judging, not proving a
hypothesis. I am sure Mr. Edwards judged his statement to be ok. ;-)
Herman
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
Behalf Of Jacob Keller
Dear Jacob,
You are overinterpreting, the statement is about judging, not proving a
hypothesis. I am sure Mr. Edwards judged his statement to be ok.
I guess there is a good likelihood that you are right, but who am I to
judge?
JPK
Herman
--
*From:* CCP4
You are the one who should judge your statement, but it looks plausible
to me.
Now that I think of it: why do we need referees if every scientist
should judge their own hypothesis? Publication will be a lot faster if
we no longer need to heed the remarks of some grumpy referees and send
in
Going back to the initial question.
I would recommend looking at AFITT
http://www.eyesopen.com/afitt
Works like a dream (in certain cases).
Jürgen
P.S. I wish I had some stocks from them but I don't
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Hi Ed,
You can have both types of error in a single experiment, however you
cannot determine
statistical (precision or as Ian says uncontrollable) error with one
experiment. The manufacturer
will usually give some specs on the pipette, 6ul +/- 1ul. In order to verify
the specs
you would
On Mon, 11 Mar 2013 11:46:03 -0400, Ed Pozharski epozh...@umaryland.edu wrote:
...
Notice that I
only prepared one sample, so if on that particular instance I picked up
4.8ul and not 5.0ul, this will translate into systematically
underestimating protein concentration, even though it could have
Dear All,
For any small molecule crystallographers who may read this board, the
Yale Chemistry Biophysical Instrumentation Center has a position
available. Besides performing service crystallography the successful
applicant will cooperate with other CBIC staff in the maintenance of
Thank you very much to all those who suggested a way out for our situation. We
have so far refined the occupancies on phenix and the ligand shows an uniform
occupancy of 0.8 post the refinement. The B-factors of the ligand are around 20
(atleast for the regions with a well defined electron
Frontiers in Neutron Structural Biology
Oak Ridge National Laboratory Spallation Neutron Source
April 16-18, 2013
REMINDER - Registration deadline soon approaching.
Deadline Dates: The deadline for application is March 15, 2013, unless you
qualify for one of the following exceptions:
The
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