I'd say they are 1 bit each, since they are the answer to a yes-or-no
question.
-James Holton
MAD Scientist
On 2/27/2020 6:32 PM, Keller, Jacob wrote:
How would one evaluate the information content of systematic absences?
JPK
On Feb 26, 2020 8:14 PM, James Holton <jmhol...@lbl.gov> wrote:
In my opinion the threshold should be zero bits. Yes, this is where
CC1/2 = 0 (or FSC = 0). If there is correlation then there is
information, and why throw out information if there is information to
be had? Yes, this information comes with noise attached, but that is
why we have weights.
It is also important to remember that zero intensity is still useful
information. Systematic absences are an excellent example. They have
no intensity at all, but they speak volumes about the structure. In a
similar way, high-angle zero-intensity observations also tell us
something. Ever tried unrestrained B factor refinement at poor
resolution? It is hard to do nowadays because of all the safety
catches in modern software, but you can get great R factors this way.
A telltale sign of this kind of "over fitting" is remarkably large
Fcalc values beyond the resolution cutoff. These don't contribute to
the R factor, however, because Fobs is missing for these hkls. So,
including zero-intensity data suppresses at least some types of
over-fitting.
The thing I like most about the zero-information resolution cutoff is
that it forces us to address the real problem: what do you mean by
"resolution" ? Not long ago, claiming your resolution was 3.0 A meant
that after discarding all spots with individual I/sigI < 3 you still
have 80% completeness in the 3.0 A bin. Now we are saying we have a
3.0 A data set when we can prove statistically that a few
non-background counts fell into the sum of all spot areas at 3.0 A.
These are not the same thing.
Don't get me wrong, including the weak high-resolution information
makes the model better, and indeed I am even advocating including all
the noisy zeroes. However, weak data at 3.0 A is never going to be as
good as having strong data at 3.0 A. So, how do we decide? I
personally think that the resolution assigned to the PDB deposition
should remain the classical I/sigI > 3 at 80% rule. This is really
the only way to have meaningful comparison of resolution between very
old and very new structures. One should, of course, deposit all the
data, but don't claim that cut-off as your "resolution". That is just
plain unfair to those who came before.
Oh yeah, and I also have a session on "interpreting low-resolution
maps" at the GRC this year.
https://www.grc.org/diffraction-methods-in-structural-biology-conference/2020/
So, please, let the discussion continue!
-James Holton
MAD Scientist
On 2/22/2020 11:06 AM, Nave, Colin (DLSLtd,RAL,LSCI) wrote:
Alexis
This is a very useful summary.
You say you were not convinced by Marin's derivation in 2005. Are you
convinced now and, if not, why?
My interest in this is that the FSC with half bit thresholds have the
danger of being adopted elsewhere because they are becoming standard
for protein structure determination (by EM or MX). If it is used for
these mature techniques it must be right!
It is the adoption of the ½ bit threshold I worry about. I gave a
rather weak example for MX which consisted of partial occupancy of
side chains, substrates etc. For x-ray imaging a wide range of
contrasts can occur and, if you want to see features with only a
small contrast above the surroundings then I think the half bit
threshold would be inappropriate.
It would be good to see a clear message from the MX and EM
communities as to why an information content threshold of ½ a bit is
generally appropriate for these techniques and an acknowledgement
that this threshold is technique/problem dependent.
We might then progress from the bronze age to the iron age.
Regards
Colin
*From:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *On Behalf Of
*Alexis Rohou
*Sent:* 21 February 2020 16:35
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] [3dem] Which resolution?
Hi all,
For those bewildered by Marin's insistence that everyone's been
messing up their stats since the bronze age, I'd like to offer what
my understanding of the situation. More details in this thread from a
few years ago on the exact same topic:
https://mail.ncmir.ucsd.edu/pipermail/3dem/2015-August/003939.html
<https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/pipermail/3dem/2015-August/003939.html__;!!Eh6p8Q!TK-tIY-zm5coRu74uWMkIJkTFWNz4-1ibr1oaahxT_2BAAetUTMNdfRqUCmIsJF61uc$>
https://mail.ncmir.ucsd.edu/pipermail/3dem/2015-August/003944.html
<https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/pipermail/3dem/2015-August/003944.html__;!!Eh6p8Q!TK-tIY-zm5coRu74uWMkIJkTFWNz4-1ibr1oaahxT_2BAAetUTMNdfRqUCmIPu-nRBo$>
Notwithstanding notational problems (e.g. strict equations as opposed
to approximation symbols, or omission of symbols to denote
estimation), I believe Frank & Al-Ali and "descendent" papers (e.g.
appendix of Rosenthal & Henderson 2003) are fine. The cross terms
that Marin is agitated about indeed do in fact have an expectation
value of 0.0 (in the ensemble; if the experiment were performed an
infinite number of times with different realizations of noise). I
don't believe Pawel or Jose Maria or any of the other authors really
believe that the cross-terms are orthogonal.
When N (the number of independent Fouier voxels in a shell) is large
enough, mean(Signal x Noise) ~ 0.0 is only an approximation, but a
pretty good one, even for a single FSC experiment. This is why, in my
book, derivations that depend on Frank & Al-Ali are OK, under the
strict assumption that N is large. Numerically, this becomes apparent
when Marin's half-bit criterion is plotted - asymptotically it has
the same behavior as a constant threshold.
So, is Marin wrong to worry about this? No, I don't think so. There
are indeed cases where the assumption of large N is broken. And under
those circumstances, any fixed threshold (0.143, 0.5, whatever) is
dangerous. This is illustrated in figures of van Heel & Schatz
(2005). Small boxes, high-symmetry, small objects in large boxes, and
a number of other conditions can make fixed thresholds dangerous.
It would indeed be better to use a non-fixed threshold. So why am I
not using the 1/2-bit criterion in my own work? While numerically it
behaves well at most resolution ranges, I was not convinced by
Marin's derivation in 2005. Philosophically though, I think he's
right - we should aim for FSC thresholds that are more robust to the
kinds of edge cases mentioned above. It would be the right thing to do.
Hope this helps,
Alexis
On Sun, Feb 16, 2020 at 9:00 AM Penczek, Pawel A
<pawel.a.penc...@uth.tmc.edu <mailto:pawel.a.penc...@uth.tmc.edu>> wrote:
Marin,
The statistics in 2010 review is fine. You may disagree with
assumptions, but I can assure you the “statistics” (as you call
it) is fine. Careful reading of the paper would reveal to you
this much.
Regards,
Pawel
On Feb 16, 2020, at 10:38 AM, Marin van Heel
<marin.vanh...@googlemail.com
<mailto:marin.vanh...@googlemail.com>> wrote:
***** EXTERNAL EMAIL *****
Dear Pawel and All others ....
This 2010 review is - unfortunately - largely based on the
flawed statistics I mentioned before, namely on the a priori
assumption that the inner product of a signal vector and a
noise vector are ZERO (an orthogonality assumption). The
(Frank & Al-Ali 1975) paper we have refuted on a number of
occasions (for example in 2005, and most recently in our
BioRxiv paper) but you still take that as the correct
relation between SNR and FRC (and you never cite the
criticism...).
Sorry
Marin
On Thu, Feb 13, 2020 at 10:42 AM Penczek, Pawel A
<pawel.a.penc...@uth.tmc.edu
<mailto:pawel.a.penc...@uth.tmc.edu>> wrote:
Dear Teige,
I am wondering whether you are familiar with
Resolution measures in molecular electron microscopy.
Penczek PA. Methods Enzymol. 2010.
Citation
Methods Enzymol. 2010;482:73-100. doi:
10.1016/S0076-6879(10)82003-8.
You will find there answers to all questions you asked
and much more.
Regards,
Pawel Penczek
Regards,
Pawel
_______________________________________________
3dem mailing list
3...@ncmir.ucsd.edu <mailto:3...@ncmir.ucsd.edu>
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
<https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwMFaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=yEYHb4SF2vvMq3W-iluu41LlHcFadz4Ekzr3_bT4-qI&m=3-TZcohYbZGHCQ7azF9_fgEJmssbBksaI7ESb0VIk1Y&s=XHMq9Q6Zwa69NL8kzFbmaLmZA9M33U01tBE6iAtQ140&e=>
_______________________________________________
3dem mailing list
3...@ncmir.ucsd.edu <mailto:3...@ncmir.ucsd.edu>
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
<https://urldefense.com/v3/__https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem__;!!Eh6p8Q!TK-tIY-zm5coRu74uWMkIJkTFWNz4-1ibr1oaahxT_2BAAetUTMNdfRqUCmI7LD77u4$>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1__;!!Eh6p8Q!TK-tIY-zm5coRu74uWMkIJkTFWNz4-1ibr1oaahxT_2BAAetUTMNdfRqUCmI1pndYoE$>
--
This e-mail and any attachments may contain confidential, copyright
and or privileged material, and are for the use of the intended
addressee only. If you are not the intended addressee or an
authorised recipient of the addressee please notify us of receipt by
returning the e-mail and do not use, copy, retain, distribute or
disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual
and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any
attachments are free from viruses and we cannot accept liability for
any damage which you may sustain as a result of software viruses
which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in
England and Wales with its registered office at Diamond House,
Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE,
United Kingdom
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1__;!!Eh6p8Q!TK-tIY-zm5coRu74uWMkIJkTFWNz4-1ibr1oaahxT_2BAAetUTMNdfRqUCmI1pndYoE$>
------------------------------------------------------------------------
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1__;!!Eh6p8Q!TK-tIY-zm5coRu74uWMkIJkTFWNz4-1ibr1oaahxT_2BAAetUTMNdfRqUCmI1pndYoE$>
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
