The characters on my car license plate are in one sense highly improbable -
billions-to-one against. In another sense they are normal and probable
because there is nothing special about those characters.
However if I ordered a new car and it was delivered with a license plate
that included my
f of Pavel Afonine
Date: Wednesday, November 9, 2022 at 6:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] outliers
[This email originated from outside of OSU. Use caution with links and
attachments.]
This is best illustrated by Ramachandran "outliers",
which are perfectly supported
>
> This is best illustrated by Ramachandran "outliers",
> which are perfectly supported by electron density.
>
Indeed, and 3NOQ is one of my favorite examples of that, an outlier isn't
necessarily equates to wrong! However, I think torsion angles (eg, phi/psi)
are much more flexible than
Dear all,
what I am missing in this whole thread is the question
on what is the "true" value of a given bond distance. So
far, everybody seems to assume that the "ideal" value
is equivalent to the "true" value, and that deviations
from the ideal values must therefore be outliers.
I challenge
And now it is time for an "old man story". Back in the early 1990's
the Brookhaven PDB started to worry about "validating" the models being
deposited. One of the things they implemented was to add to the header
of the PDB a complete list of all bond lengths and angles that deviated
from
The second part of your question has to do with assessing the
probability of correctness of a model by comparing the distribution of
the individual values of geometry items with the distribution observed
in large sets of high quality crystal structures. Certainly, if your
model has many
On Tue, 8 Nov 2022 15:25:03 -0800, James Holton wrote:
>Thank you Ian for your quick response!
>
>I suppose what I'm really trying to do is put a p-value on the
>"geometry" of a given PDB file. As in: what are the odds the deviations
>from ideality of this model are due to chance?
>
>I am
Let's say you have decided that you want to know if the CA-CB bond
of residue 123 in your favorite protein differs from the expected value
for that type of bond. You solve the structure and refine a model
against your crystallographic data, then look at residue's 123 CA-CB
bond and find
a crystal structure
where one significant outlier was “masked” by nearly perfect rest of the model.
Best regards,
Petr
Od: CCP4 bulletin board za uživatele James Holton
Odesláno: Wednesday, November 9, 2022 12:51 AM
Komu: CCP4BB@JISCMAIL.AC.UK
Předmět: Re: [ccp4bb] outliers
Thank you
Thank you for this.
Hmmm.
Interesting, and good to know the expected distribution of extreme values.
However, what I'm more worried about is how to evaluate the other 999
points? Lets say I'm trying to compare two 1000-member sets (A and B)
that both have an extreme value of 3, but for the
Hi James,
This is what you need.
https://en.wikipedia.org/wiki/Generalized_extreme_value_distribution
The distribution of a maximum of 1k random variates looks like this, and
the (fitted by eye) analytical distribution associated with it seems to
have a decent fit - as expected.
[image:
Thank you Ian for your quick response!
I suppose what I'm really trying to do is put a p-value on the
"geometry" of a given PDB file. As in: what are the odds the deviations
from ideality of this model are due to chance?
I am leaning toward the need to take all the deviations in the
, or a completely different one. I know you will do a fluorescence
scan in your MAD beamline to sort it out
Best wishes,
Joao
-Original Message-
From: CCP4 bulletin board On Behalf Of James Holton
Sent: Tuesday, November 8, 2022 5:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [EXTERNAL] [ccp4bb
Hi James
I don't think it's meaningful to ask whether the deviation of a single bond
length (or anything else that's single) from its expected value is
significant, since as you say there's always some finite probability that
it occurred purely by chance. Statistics can only meaningfully be
OK, so lets suppose there is this bond in your structure that is
stretched a bit. Is that for real? Or just a random fluke? Let's say
for example its a CA-CB bond that is supposed to be 1.529 A long, but in
your model its 1.579 A. This is 0.05 A too long. Doesn't seem like
much, right? But
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