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 revision after revision. Also the number of publications will
increase significantly if every scientist is allowed to judge their own
papers!
HS
________________________________
From: Jacob Keller [mailto:[email protected]]
Sent: Tuesday, March 12, 2013 4:14 PM
To: Schreuder, Herman R&D/DE
Cc: [email protected]
Subject: Re: [ccp4bb] validating ligand density
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 bulletin board
[mailto:[email protected]] On Behalf Of Jacob Keller
Sent: Tuesday, March 12, 2013 3:44 PM
To: [email protected]
Subject: Re: [ccp4bb] validating ligand density
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.
There must be a lot of thinking behind this
statement--while it seems plausible, it seems far from proven prima
facie. Also, it assumes that the scientist is not a statistician.
Jacob
Btw, the book is good reading.
Best, BR
-----Original Message-----
From: CCP4 bulletin board
[mailto:[email protected]] On Behalf Of Robbie
Joosten
Sent: Tuesday, March 12, 2013 10:03 AM
To: [email protected]
Subject: Re: [ccp4bb] validating ligand
density
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
(and the maps themselves of course),
they will tell you whether you
misidentified your ligand. Occupancy
refinement in Refmac can also help you:
if the occupancy drops a lot
something is wrong. That can be partial
binding (not that much of a problem)
or worse, a ligand that isn't there. By
the way, I've been playing with
that recently and some ligands/hetero
compounds in the PDB were so
incredibly 'not there' that Refmac would
crash (that bug seems to be fixed
in the latest version).
HTH,
Robbie
> -----Original Message-----
> From: CCP4 bulletin board
[mailto:[email protected]] On Behalf Of
> R.Srinivasan
> Sent: Monday, March 11, 2013 23:03
> To: [email protected]
> Subject: [ccp4bb] validating ligand
density
>
> Hello all,
>
> We co-crystallized an
inactive variant of our enzyme in
> the
presence of
> substrate and have determined the
structure at 1.85A.
>
> Now, we want to validate
the fitting of the ligand into
> the
electron
> density. We tried validating using the
difference map (2Fo-Fc) after
refining
> the structure without the ligand. But,
it is still a bit inconclusive
> if
the density
> fits the ligand.
>
> It would be very kind to
know if there are tools for
validating this
> electron density. We were excited
about twilight but turns out it can
> only
be
> used with deposited structure.
>
>
> We will appreciate your
help and suggestions.
>
>
> Many thanks,
> Srinivasan
--
*******************************************
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: [email protected]
*******************************************
--
*******************************************
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: [email protected]
*******************************************
