Given Cu, yes, the five M edges between 2.3keV and 3.6keV contribute a
continuum transition signal of the 8e- you initially referred to.
-Original Message-
From: Jacob Keller [mailto:j-kell...@fsm.northwestern.edu]
Sent: Wednesday, June 06, 2012 12:35 PM
To: b...@hofkristallamt.org
Cc:
I do not seem to understand the meaning of fixing. Fixing something can
mean
a) repairing it, implying that something was broken or amiss. Lack of
experimental information expressed as omission of atoms is not something
that needs fixing.
b) keeping it constant. Like in having
It would be desirable to actually HAVE the cell information in the cif file,
if simply for assuring/checking consistency between model and data.
Maybe something for the PDB to contemplate
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Don't worry. High B-factor just means that the probability of the atoms
being at the specified coordinate position is low, for whatever reason.
In most cases this is completely normal and often indicative of solvent
exposed surface residues, and a look at the electron density will
show whether
with Mozilla - http://enigmail.mozdev.org/
iD8DBQFPhFP3UxlJ7aRr7hoRAj4HAKDpHCsN+tBKhDAcOYmIe5c58ThG+gCeMujG
pAJxRNuJHE4+oFRPSYx4bnc=
=s3uw
-END PGP SIGNATURE-
--
-
Bernhard Rupp (Hofkristallrat a. D)
001 (925) 209-7429
+43 (676
Dear CCPx administrators:
I just notice that on
/www.ccp14.ac.uk/ccp/web-mirrors/llnlrupp/cvs/Rupp/rupp.html
a deprecated web page from the early 2000s (!) that causes confusion exists
on a mirror of the LLNL site dead since 2005.
I cannot find a responsible contact for CCP14 since Lachlan's
You never know when a forgotten slip of the mouse when using AutoDep ten
years ago will come back to haunt you.
On the paper James refers to and found the data, added mystery was that the
postdoc who may have slipped disappeared w/o much of trace and the PI died.
Dan was the only survivor. Still
that address space is the issue here if they are.
Maybe the paranoia-checkers in windows slow everything down
although I did not see any resources overwhelmed...
Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b
I also don't really worry about the images as a primary means of fraud
prevention, although such may be
a useful side effect. These cases are spectacular but so rare that it indeed
would not primarily justify the effort.
That it can be a useful political instrument to make that argument and get
Ojweh
c) Discarding your primary data is generally considered bad form...
Agreed, but it is a big burden on labs to maintain archives of their raw
data indefinitely.
Even IRS allows to discard them after some time.
But you DO have to file in the first place, right? How long to keep is an
, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt
I have RHEL62-64 in a win 7-64 8GB desktop VMware installation. CCP4, ccp4i,
coot, and shelxcde beta executables run fine.
There were issues with the coot package installation due to unresolved
dependencies
and my ignorance thereof, but I think a working RHEL62-64 compatible package
is available
Orcus,
if you put yourself persistently into the face of guys who play hard, you
need to learn to
take a few hits and shake it off. Maybe a little retrospection on why your
postings might
perhaps possibly maybe perceived as somewhat self-promoting and ungracious
could be helpful.
The
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
Thanks of your education. I got it.
By the way, what does Orcus mean here?
Regards,
Kevin
On Tue, Apr 3, 2012 at 5:11 PM, Bernhard Rupp (Hofkristallrat a.D.)
hofkristall...@gmail.com wrote:
Guys,
http://www.youtube.com/watch?v=CobZuaPMQHw
second 9 in this 22 sec video
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gerard
DVD Kleywegt
Sent: Monday, April 02, 2012 8:04 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] one
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Bernhard Rupp (Hofkristallrat a.D.)
Sent: Sunday, April 01, 2012 06:06
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
Hofkristallrat außer Dienst, is written as Bernhard - unless you are
referring to some other
in a collaboration?
Maybe you could just
put a link on your page?
JPK
==Original message text===
On Fri, 17 Aug 2007 3:24:45 pm CDT Bernhard Rupp wrote:
The PDB is missing a business opportunity. If authors pay
1000s of dollars for publication in high impact journals,
they might as well
orcus impudens
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kendall
Nettles
Sent: Sunday, April 01, 2012 1:28 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] very informative - Trends in Data Fabrication
What is the single Latin word for troll?
Kendall
On
Hi Fellow BBers,
I wish to point out that
a) this is not an April fools joke,
b) but on the other hand it shows (a little buried in the
recommendations, and misspelled AFTER proofing) that people who properly do
catalogue and preserve images actually can fix deposition errors
This is an unresolved problem, and no real satisfactory solution exists,
because the underlying reasons for zero occupancy can be different.
For people who understand this and look at electron density, it is not a
problem. For users who rely on some graphics program
displaying only atom
Hofkristallrat außer Dienst, is written as Bernhard - unless you are
referring to some other guy with a french name Bernard.
As one may extrapolate given my recent paper, I have been called names a lot
worse
.
Ø And the book indeed is a bible of xtallography.
Enough of this - it
Btw,
Table 1 would have fooled me as referee.
Not if the bulk solvent parameters would be reported or validated. See
recommendations.
Best, BR
phenix.refine allows any number of alternate conformers.
Hmm. quoting our old friends from the validation circuit: Where freedom
is given, liberties will be taken
BR
As you observe, radiation damage is local, but the effect is - to different
extent - on all Fs i.e. global (all atoms and their damage contribute to
each hkl).
So one would need additional local parameters (reducing N/P) if you want to
address it as such, your use of occupancy is an example (even
I can't imagine the results would be very different for protein-DNA vs.
protein-RNA.
The reason protein-nucleic acids is an extra category in mattprob is largely
due to poorer statistics
resulting from limited sample size and hence no reliable resolution dependence
can be computed.
In
Ø Some of these 'water' have more than 4 contacts, I would consider them as
'false'.
How about bifurcated hydrogen bonds?
BR
Why, in the first place, do you feel an urge to concentrate your protein
above 3 mg/ml ?
For crystallization, the concentration needs to be
a) high enough to achieve supersaturation, meaning close enough to the
maximum solubility in a given buffer so that the precipitant can drive the
Ø in 2004. Of the 1000 entries that listed [protein], 46 proteins were
crystallized below 3.1 mg/ml.
That is not necessarily the success rate for low concentrations, which we
actually would like to have. We would need negatives for 3 for to give a
correct answer. I guess even occurrence
You might get lucky by setting up crystallization plates, but chances are
you won't get very useful information from them, especially if your
aggregated protein is soluble.
I seem to fail to understand how crystallization plates would give
information in the not-special case of protein
Well, depends on what 'aggregated' really means. If it implies reasonably
weak oligomerization interaction - and it
might not be too strong given that the oligomers remain soluble - a
chaotropic crystallization agent (on the
extreme end certain high salts, consult Hofmeister for chaotropicity)
Btw, re other sources of deviation: Molprobity does not report geometry
deviations beyond CB. The RUN500 command from CCP4i does.
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale
Tronrud
Sent: Thursday, February 16, 2012 10:56 AM
To:
For MIR, you also need to weigh your options.
If you want to use anomalous signal for SIRAS/MIRAS, you may want to be above
the most prominent or at least a useful edge of your HA.
On the other hand, being above an HA edge increases you chance of serious
radiation damage. Sometimes you may need
It might be worthwhile to follow the thread of similar problems on the coot
mailing list
and a generic solution on the coot-wiki, like
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Example:_in
stalling_a_64bit_nightly_CentOS5_binary_build_on_64bit_SL6.1
BR
-Original
),
the real part is always centrosymmetric,
while the complex (phase) part is not.
Probably needs some tweaking to be really useful for presentation purpose.
BR
-Original Message-
From: Bernhard Rupp (Hofkristallrat a.D.) [mailto:hofkristall...@gmail.com]
Sent: Friday, January 06, 2012
, Jan 30, 2012 at 11:10 AM, Bernhard Rupp (Hofkristallrat a.D.)
hofkristall...@gmail.com wrote:
Dear All,
when I plot bulk solvent B and K extracted from EDS, an improbable and
bimodal distribution appears.
In the B_sol vs k_sol PDF a sharp line of values with B-sol of 70 appears
(B-axis left
For the history buffs and crystallographers needing some RR and chill-out,
an interesting historic fiction read about the era of Newton and Leibnitz
and the foundation of the Royal Society is the Baroque cycle by Neil
Stevenson.
http://en.wikipedia.org/wiki/The_Baroque_Cycle
Cryptonomicon,
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
b...@hofkristallamt.org
http://www.ruppweb.org/
-
No animals were hurt or killed during the
production of this email.
-
You might want to look at some images of side chain electron density.
http://www.ruppweb.org/garland/gallery/Ch2/index_2.htm
BR
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dialing
Pretty
Sent: Friday, January 13, 2012 2:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Dear All,
I read an interesting statement in an NMR review:
regions of a protein or
DNA ⁄ RNA molecule that are flexible in the crystal do
not provide coherent X-ray scattering and hence do
not contribute to the final electron density map. Thus,
for all intents and purposes, they can
] NMR review
Dear Bernhard,
Am 12.01.12 10:30, schrieb Bernhard Rupp (Hofkristallrat a.D.):
Dear All,
I read an interesting statement in an NMR review:
regions of a protein or
DNA / RNA molecule that are ?exible in the crystal do not provide
coherent X-ray scattering and hence do
This may give some idea:
Illustration of a molecule and its cosine transform:
http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph
y_Fig_6-16.htm
and sampled by lattice points
http://www.ruppweb.org/garland/gallery/Ch6/pages/Biomolecular_Crystallograph
So what's new?
Alzheimer's and late night senile dementia :-)
BR
PS: nice site!
-Original Message-
From: Ian Tickle [mailto:ianj...@gmail.com]
Sent: Monday, January 02, 2012 4:34 AM
To: b...@hofkristallamt.org
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] refmac low resolution
!
6 NONE1.637.3 361 96.40 8.84 8.84 28.66 1.99 Q
SIGFP
I have noticed that other PDB/sf file sets (not mine) seem to be affected as
well.
Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571
Dear Garib,
thank you for the quick response despite (or because of) the holidays. Ill
try to summarize because I am not sure I understand yet, and it might be
useful for all :
Ø Partial structure mask bulk solvent parameters. Mask bulk solvent B value
is in addition to protein B value.
) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.711
Explanation/intuition would be much appreciated.
Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
hofkristall...@gmail.com
b
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt or killed during the
production of this email.
-
Hi Fellows,
I am looking for some advice re LN2 autofill. I want to automatically refill
an open special-use foam Dewar
on the crystal harvesting robot from an unpressurized secondary storage
Dewar. We found this system
http://www.norhof.com/fillingexample.html
and it seems to do what we need
I am not sure this service is maintained anymore, but given that with
automated model building pretty much the same can be achieved nowadays (pus
benefit of a model), the ARP/wARP server in Hamburg is a well-working and
up-to-date alternative.
BR
From: CCP4 bulletin board
Hi Fellows,
here is your chance to vote for a crystallographer in the People's Choice
education program contest:
http://us2.campaign-archive2.com/?u=3e43dd9d1724b97d2bc286881id=485f01c36b;
e=76452e4682
Best regards, BR
-
Bernhard
If the difference in likelihood is quite small then you cannot distinguish
between a RB shifted model and one w/o the shift and that shift must be
insignificant (in a statistical sense.) If the likelihood is better when
the shift is allowed then the shift is significant.
That of course is
What is your resolution? The gap is usually wider at lower resolution.
Here a figure displaying distribution gap stats:
http://www.ruppweb.org/garland/gallery/Ch12/pages/Biomolecular_Crystallograp
hy_Fig_12-24.htm
Cheers, BR
-Original Message-
From: CCP4 bulletin board
If for example your presumed coil is differently bent than your search
probe, overall rmsd is high and MR will likely fail. But maybe ARCIMBOLDO
with helix fragments might do at 1.65A? George or Isabel will have a better
answer.
Good luck, BR
PS: And may San Matheus de las Coefficientes listen
Hi Fellows,
I was attending the inaugural meeting of the Data Deposition Working Group
in Madrid. They are aware of the various points raised, and a
document/recommendation has been prepared that I assume will be soon made
public (John?). Amount of data seems not an insurmountable technical
in Phenix ?
Jürgen
On Oct 16, 2011, at 4:20 PM, Bernhard Rupp (Hofkristallrat a.D.) wrote:
REPROCESS_PDB
..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research
Ø Do you mean to reprocess determination of I and sig(I) from the
diffraction images automatically??? Or just to get an access to the raw
data?
Reprocessing the images with the to-be-developed new software that will
process the information in the data in full, and then using the
Ø Not if you are interested in scattering that falls between reciprocal
lattice maxima, or if you want to preserve the possibility of applying
future data reduction packages.
Yep, this is exactly what I expressed in my original statement:
diffuse solvent contributions, commensurate and
it will be before we all travel to work with jetpacks or flying cars
http://www.popularmechanics.com/science/4247253
Thunderbolt Aerosystems, based in California, plans to start selling its
ThunderPack TP-R2G2 rocket belt to customers this summer.
the editor should agree to publish the paper swiftly in advance before the
data become accessible to reviewers.
This seems to miss the point - how is the reviewer then supposed to judge
the map?
BR
Nian
On Wed, Aug 10, 2011 at 5:25 PM, Filip Van Petegem
filip.vanpete...@gmail.com
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
--
Knowledge: When you know a thing, to know that you know
: Re: [ccp4bb] Modified residue list
On Tuesday, July 26, 2011 10:46:34 am Bernhard Rupp (Hofkristallrat a.D.)
wrote:
Dear All,
Is there a simple way (or already an existing list) to extract/parse
from the heterodictionaries or monomer libraries which 3-letter
symbols are actually modified
If you are eligible, I'd highly recommend the EMBO courses in Europe or the
CSHL courses in the US on those subjects. Reading is a good start but will
not be enough if you want to do real work.for strategy considerations, there
is always Ch 3 and 4 in le livre.
Best, BR
From: CCP4 bulletin
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
--
-
Bernhard Rupp (Hofkristallrat a. D)
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org
are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.
--
-
Bernhard Rupp (Hofkristallrat a. D)
001 (925) 209-7429
+43
Easiest way:
CCP4i
Reflection Data Utilities
Convert to MTZ
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Madhu
shankar Madhu shankar
Sent: Thursday, June 23, 2011 5:26 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Convert .cif to mtz
HI,
A coordination distance table (metals, Cl) is in Marjorie Harding's papers
1. Harding M (2006) Small revisions to predicted distances around metal
sites in proteins. Acta Crystallogr. D62(6), 678-682.
2. Harding M (2004) The architecture of metal coordination groups in
proteins. Acta Crystallogr.
Given that the water and the barium seem to have the same electron density
on image electron
png Id look careful at relative density levels,
occupancies, B-factors etc. Often the situation becomes clearer during later
stages of refinement.
Peripherally, I also do not exactly understand the
Thx Clemens, - my indexing gives the same setting, correct is -a -b c
BR
-Original Message-
From: Clemens Vonrhein [mailto:vonrh...@globalphasing.com]
Sent: Wednesday, June 08, 2011 9:06 AM
To: Bernhard Rupp (Hofkristallrat a.D.)
Subject: Re: [ccp4bb] Change cell parameter
Hi Bernhard
http://en.wikipedia.org/wiki/Propagation_of_uncertainty
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
capricy gao
Sent: Saturday, June 04, 2011 10:45 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question about the statistical analysis-might be a bit off
topic
I have limited cautionary experiences with Lec1 CHO expression, although with a
highly and complex glycosilated protein. Subsequent glycan analysis showed that
the glycans are indeed more homogeneous and less branched, but not exclusively
the Man5GlcNac2 type that are reported/expected. There
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt or killed during the production of this email.
-
Windows CCP4i:
The log (attached) for mtz file to user conversion states a format error,
when in fact the output file was locked by another application. Format is
ok.
Not tragic, but confusing.
Best regards, BR
-
Bernhard Rupp
001
I have never heard of this happening (or seen a structure where there was
density for this type of adduct)
Maybe it is kind of textbook-knowledge? BMC p48 Fig 2-27
http://www.ruppweb.org/garland/gallery/Ch2/index_2.htm
BR
Does anyone know whether or not this is possible, and why it does
This has been discussed multiple times on bb, also BMC p640.
The restraint target standard uncertainty
provides an upper limit54 for a reasonable bond or angle r.m.s.d. from
targets
within the model (approximately 0.02 Å and 1.9deg, respectively), but makes
no
further assumption where these
Thus my feeling is that if one does NOT see the coords in the electron
density, they should NOT be included, and let someone else try to model
them in, but they should be aware that they are modeling them.
Joel L. Sussman
Concur. BMC p 680 'How to handle missing parts'
Best wishes, BR
Israel
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp
(Hofkristallrat a.D.) [hofkristall...@gmail.com]
Sent: Sunday, April 03, 2011 7:42 PM
Dear young (and not so young) impressionable friends of Dark Matter,
Thank you for all the kind requests for my PRL paper [1]. Unfortunately, I have
to retract the paper, but buying me a beer next time we meet might help me to
forget you ever asked for it.
One (!) respondent got it right
In my experience, the Refmac's default restraints on B-factors in side chains
are too tight and I adjust them.
Concur. See BMC p 640.
BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt or killed during the
production of this email.
-
trouble.
Best regards, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org
related to what I feel is recent revival of the significance of the R-values
because it's so handy to have one single number to judge a highly complex
nonlinear multivariate barely determined regularized problem! Just as easy as
running a gel!
Best BR
-Original Message-
From:
: ++972-3640-9407
Cellular: 0547 459 608
On Mar 3, 2011, at 18:38 , Bernhard Rupp (Hofkristallrat a.D.) wrote:
related to what I feel is recent revival of the significance of the
R-values
because it's so handy to have one single number to judge a highly
complex nonlinear multivariate barely
First of all I would ask a XDS expert for that because I don't know exactly
what stats the XDS program reports (shame on me, ok) nor what the quality of
your error model is, or what you want to use the data for (I guess
refinement - see Eleanor's response for that, and use all data).
There is one
was to be a little bit
below Rmerg 100%. At 2.3A Rmerg was 98.7% Actually, I have published
my paper in JMB. Yes, reviewers did not like that and even made me
give Rrim and Rpim etc.
Maia
Bernhard Rupp (Hofkristallrat a.D.) wrote:
First of all I would ask a XDS expert for that because I
below Rmerg 100%. At 2.3A Rmerg was 98.7% Actually, I have published
my paper in JMB. Yes, reviewers did not like that and even made me
give Rrim and Rpim etc.
Maia
Bernhard Rupp (Hofkristallrat a.D.) wrote:
First of all I would ask a XDS expert for that because I don't know
Bernhard Rupp (Hofkristallrat a.D.) wrote:
First of all I would ask a XDS expert for that because I don't know
exactly what stats the XDS program reports (shame on me, ok) nor
what the quality of your error model is, or what you want to use the
data for (I guess refinement - see Eleanor's
For those who concern themselves with such matters, the 1973 edition of
Sir Harold Jeffreys' Scientific Inference has just been reissued as a
Cambridge paperback.
Together with AFW Edwards' Likelihood this is good material for the finer
aspects of
inference I did only cursory touch in BMC chapter
Any idea where then phases came from?
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Thomas
Juettemann
Sent: Wednesday, February 09, 2011 12:16 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] First images of proteins and viruses caught with
R is a well-documented statistics package.
http://www.r-project.org/
BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Keitaro Yamashita
Sent: Sunday, February 06, 2011 2:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] adding gaussian noise
editors
have not responded so far.
Best, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org
, BR
-
Bernhard Rupp
001 (925) 209-7429
+43 (676) 571-0536
b...@ruppweb.org
hofkristall...@gmail.com
http://www.ruppweb.org/
-
No animals were hurt or killed during
to
crosscheck this in an automatic fashion (maybe PDB has some tools to do
that?) or whose responsibility it is to ensure consistency here. JBC
editors
have not responded so far.
Best, BR
-
Bernhard Rupp
001 (925) 209-7429
+43
density maps.
Ron
On Thu, 23 Dec 2010, Bernhard Rupp (Hofkristallrat a.D.) wrote:
can anyone point me to a more exact theory of distance accuracy
compared
to
optical resolution, preferably one that would apply to microscopy as
well.
Stenkamp RE, Jensen LH (1984) Resolution revisited
I find the super-resolution claims in this paper a bit of a conjuring
trick.
I think it is understood that information cannot come from nothing. You
cannot cheat in basic physics. Interestingly, I had the same discussion with
bioinformatics colleagues a short time ago. The problem is the same
can anyone point me to a more exact theory of distance accuracy compared
to
optical resolution, preferably one that would apply to microscopy as well.
Stenkamp RE, Jensen LH (1984) Resolution revisited: limit of detail in
electron density maps. Acta Crystallogr. A40(3), 251-254.
MX, BR
Oops I am outdated: Axel just emailed me that he describes an improved
coordinate estimate beyond the Rayleigh criterion in his recent paper
Schroder GF, Levitt M, Brunger AT (2010) Super-resolution biomolecular
crystallography with low-resolution data. Nature 464(7292), 1218-1222.
For the
and noise issues, I can't see any contradiction or
problem here?
Best, BR
-Original Message-
From: Ronald E Stenkamp [mailto:stenk...@u.washington.edu]
Sent: Thursday, December 23, 2010 12:06 PM
To: Bernhard Rupp (Hofkristallrat a.D.)
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb
Specific density of protein is about 1.34 g/cm3. Correct by solvent
fraction. About 600-700mg/ml for 50% for example. Compute molarity from
there.
BR
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Teresa
De la Mora
Sent: Monday, December 13, 2010 12:08 PM
To:
FYI, crystal fans. Really worth watching, and with X-mas approaching perfect
gifts for the crystals in your life. BR
From: JuanMa GarciaRuiz [mailto:juanma.garciar...@gmail.com]
Sent: Friday, December 03, 2010 10:08 AM
To: Juan Manuel García Ruiz
Subject: Juanma: The Mystery of the Giant
It seems that the Fourier cat is up to no good again..
BR
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Hubing
Lou
Sent: Wednesday, November 24, 2010 6:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] unusual diffraction spots
Dear CCP4BBer,
I recently
I looked on the web but all the software that I found require the sequence
to be the same for both structure.
most modern programs perform some kind of local-global alignment first
to define the corresponding residues and then compute the statistics.
BR
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