>>And as we often end our beer-discussions - may be all protein space groups
>>are actually true P1, just close enough to satisfy the high symmetry rules ..
>>but this is getting a bit philosophical I know ..
Could we add that all crystals are twinned, just some are in such a way as to
be a pro
Dear Crystallographers,
Does anyone know of a good biophysical way to identify or quantify sodium ion
binding to a protein, besides crystallography and ITC? Is this possible with
SPR, perhaps? Mass spec? Gel shifts? Examples would be greatly appreciated!
All the best,
Jacob Keller
How would one evaluate the information content of systematic absences?
JPK
On Feb 26, 2020 8:14 PM, James Holton 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
ay 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
Maybe there is something required for interaction that was in the buffer used
for the other binding studies, but not in your SEC buffer?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David
Briggs
Sent: Tuesday, January 21, 2014 10:52 AM
To: CCP4BB@JISCMAIL.AC.UK
Subj
Try looking into tetartohedral twinning as well--I think I may have such a
crystal, and it's tough going. And as Kay pointed out, try the various P3's.
Since I have not yet been successful in figuring my similar case out, what do
people on the list recommend as an approach to figuring this out-
Two more papers on twinning I found informative:
===
Acta Cryst. (2003). D59, 2004-2016[ doi:10.1107/S0907444903021085 ]
Twinned crystals and anomalous phasing
Z. Dauter
Abstract: Merohedral or pseudomerohedral twinning of crystals cannot be
identifie
I wonder whether flash-cooling from -10 degC would preserve those low mosaicity
values?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of mesters
Sent: Thursday, February 06, 2014 8:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Room temperature data collection
He
Dear Crystallographers,
Where can I find the definition of the R vs batch reported in scaling?
Specifically I am wondering whether it is cumulative (each new frame versus all
previous ones pooled together) or something else, and also how this metric can
have any meaning on early frames when one
What a nice idea this ITC dilution is--a great example of a wet lab technique
learned en passant on the ccp4bb.
I wonder what range of Kds could feasibly be measured with existing calorimeter
sensitivities?
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]
You could also try TCEP as a reducing agent-strong and compatible with IMAC.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Raji
Edayathumangalam
Sent: Sunday, February 16, 2014 10:58 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Trouble cleaving SUMO tag off of membr
If you need phases, you might change the salt ion(s) to something with
significant anomalous signal, i.e., Rb+, Cs+, Br-, I- instead of Na+ and Cl-.
With such high ion concentrations, you should get some really high-occupancy
sites. In any case it is sometimes handy to have experimental phases i
It seems to me some of the images may have multiple lattices and/or
pseudomerohedral twinning. Are all the spots predicted during integration? What
do the various twinning tests indicate?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Chris Fage
Sent: Sunday, Februa
(Off-list)
Dear Kay and Harry,
You mentioned difficult datasets being of interest for the ACA conference. I am
not coming, but do have some interesting datasets, viz., many datasets of a
particular crystal form of a calmodulin/peptide complex which have defied my
[not exhaustive] attempts to s
and periplasmic binding protein
families, but does anyone know of others out there?
All the best,
Jacob Keller
***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***
considerations, or something else. Maybe this does not even matter in
most cases, but it might be important in others...
All the best,
Jacob Keller
***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
>You indicate that oxygen anomalous scattering could be used; whilst this is
>applicable to chirality determination in small molecule organic
>crystallography the oxygen anomalous signal is very small and to my knowledge
>not used thus far in protein crystallography.
Perhaps I should have bee
Not sure I understand why having statistical disorder makes for streaks--does
the crystal then have a whole range of unit cell constants, with the spot at
the most prevalent value, and the streaks are the "tails" of the distribution?
If so, doesn't having the streak imply a really wide range of
>For any sample, crystalline or not, a generally valid description of
>diffraction intensity is it being a Fourier transform of electron density
>autocorrelation function.
I thought for non-crystalline samples diffraction intensity is simply the
Fourier transform of the electron density, not it
>The Fourier transform of electron density is a complex scattering amplitude
>that by the axiom of quantum mechanics is not a measurable quantity. What is
>measurable is the module squared of it. In crystallography, it is called either
F^2 (formally equal F*Fbar) or somewhat informally diffractio
>Unless you are interested in finding curious objects, what would you do with
>protein quasicrystal? The practices of macromolecular crystallography is about
>determining 3-dimensional structure of objects being crystallized. Protein
>quasicrystal are really unlikely to diffract to high enough r
to:zbys...@work.swmed.edu]
Sent: 13 March 2014 21:33
To: ccp4bb
Subject: Re: [ccp4bb] twinning problem ?
On 03/13/2014 10:55 AM, Keller, Jacob wrote:
>> Unless you are interested in finding curious objects, what would you do with
>> protein quasicrystal? The practices of macromolecular
>One can have microdomains without a significant increase in misorientation
>e.g. shift dislocations between domains. However, some misorientation is bound
>to occur. Not sure I understand your statement " And as the blocks get
>smaller, the distinction between "changing unit cell parameters" an
Can you post a better picture? Looks interesting
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joshua
Stillwell
Sent: Sunday, April 06, 2014 8:22 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] feedback on diffuse diffrac
Seems to me you've got multiple lattices as well, esp visible in the upper left
quadrant of the central tile.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Eugene
Valkov
Sent: Monday, April 07, 2014 3:17 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Continuing o
Is the following being neglected?
In a crystal with these putative mosaic microdomains, there will be
interference between microdomains at their edges/borders (at least), but since
most microdomains are probably way smaller than the coherence length of 3-10
microns, presumably all unit cells in
ning
diffraction pattern--I've seen them from time to time, and they're always of
course bad news. Anyone on the list have such a diffraction pattern handy?
JPK
On 04/25/2014 09:32 AM, Keller, Jacob wrote:
> Is the following being neglected?
>
> In a crystal with these
, 800±829. The reflexion of X-rays from
imperfect crystals
JPK
From: oliver.zel...@gmail.com [mailto:oliver.zel...@gmail.com] On Behalf Of
Oliver Zeldin
Sent: Friday, April 25, 2014 1:03 PM
To: Keller, Jacob
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder
Dear
Thanks to all—I’ve got the paper now
JPK
From: Keller, Jacob
Sent: Friday, April 25, 2014 1:58 PM
To: 'Oliver Zeldin'
Cc: CCP4BB@jiscmail.ac.uk
Subject: RE: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder
Does anyone know of a place where one can obtain this reference for free? I
wou
so,
are there particularly good ones? And if not, I wonder why proteases usually
require more sequence on the n-terminal side of the scissile bond?
All the best,
Jacob Keller
***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix
Here’s a summary of options people have sent me and some other related info I
found on my own (email traffic has slowed down, so assuming all votes are in):
-Inteins: cut themselves off/out in presence of DTT or similar. NEB sells kits.
-Sortase-His6: like inteins, but activated by Ca++ or trig
Attenuate the beam and take many more frames such that you get a full dataset,
albeit at slightly lower resolution, before the metals go away. In other words,
reduce dose/degPhi.
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dean
Derbyshire
Sent: Wednesday, April 30
Dear Pilatus/Radiation Damage Cognoscenti,
I read a few years ago, before the advent of Pilatus detectors, that the best
strategy was a sort of compromise between number of images and detector readout
noise "overhead." I have heard that Pilatus detectors, however, have
essentially no readout no
I myself have never seen a separate peak that was a single sulfur atom.
I've seen, in a moderately-radiation-damaged dataset, little shards of
anomalous scattering density in Phaser-generated LLG maps. They were in the
interior of the protein, and the closest possible atoms were sulfurs. They w
S. Cass Ave.
Lemont, IL 60439
Tel: (630)252-0665
Fax: (630)252-0667
rsanishv...@anl.gov<mailto:rsanishv...@anl.gov>
From: CCP4 bulletin board [CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>]
on behalf of Keller, Jacob
[kell...@janelia.h
Or "space gRupps?"
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim
Pflugrath
Sent: Friday, May 02, 2014 8:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Confusion about space group nomenclature
After all this discussion, I think that Bernhard can now lay the clai
Dear Crystallographers (teleology-haters exempt here),
Does anyone know of any references discussing teleology of inverted repeats in
transporters, i.e., what design sense does it make to use this architecture,
why is it so common even in the absence of sequence similarity? Is there some
underl
Dear Crystallographers,
In a former lab we had a script which would read DALI output, automatically
download the structurally-similar proteins, superimpose them, and color by
regions superimposed. That was in the days of O. Does anyone have a
similar-functioning script for CCP4MG, pymol, or oth
The b and c cell constants look remarkably similar
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read
Sent: Thursday, May 08, 2014 3:41 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] stalled refinement after MR solution
Hi Yarr
Just a thought—is the reducing agent changing pH? Also, is your protein a
metal-binder?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of zhuqing
ouyang
Sent: Monday, May 12, 2014 12:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off topic, complex precipitate in redu
Well, this is of only possible relevance, but in a previous lab, we used sf9
cells/media quite a bit, and there was always an issue similar to this, due to
[we thought] ferritin being secreted into the medium, and sucking up the
metals. Many, in fact, crystallized ferritin this way by mistake!
Did you look at the maps for extra density/molecules?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Matthew
Bratkowski
Sent: Monday, May 19, 2014 4:48 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Issue with Molecules per Asymmetric Unit for Molecular
Replacemen
Dear Crystallographers,
I have a feeling that Moire finges are the real-space equivalent of the Laue
zones in reciprocal-space, and this seems like a very basic idea that must have
been explored--anyone know of a source connecting the mathematico-physical
dots? Or do the dots not connect?
JPK
Dear Crystallographers,
Is anyone aware of a relationship between H-bond distance and energy thereof,
maybe with a little geometry and +/- charge thrown in? I am looking at a
structure with many H-bonds to a ligand, and wondered about the relative
importance of each.
JPK
*
Why not try direct methods on both SG options, and maybe P1 as well? Depending
on the wavelength and multiplicity, you might also have some good anomalous
signal from the P's.
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia
I know you mentioned trying buffer components, but it does look a lot like TRIS
to me, maybe a different conformation than you’re modelling?
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ash
The one I don't get is why not pay reviewers? $1000 per review? If you look at
publishers' profit margins, you will see that they can afford it. I actually
think the scientific community should go on a "review strike" until reviewers
get paid.
JPK
++
one final aspect is: who gets the money? surely the universities etc. should
get it, not us: the taxpayer pays us already.
best,
jon
-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller,
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
Wow, something really happened! I wonder how many citations of those
articles/structures are out there? 1000? I hadn't realized it was more than
just that Nature paper. I hope nothing important is built on them.
JPK
+
Jacob Pearson Keller
Research
>>But there is no rule without exception,
Well, occasionally there is.
JPK
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
I deposited a dataset on SBGrid from a calmodulin-peptide complex which has
some "nice" features: merohedral twinning (with variable twin fraction in the
same dataset) and unavoidable detector cutoffs. It's relatively easy to
integrate, but solving is somewhat harder. There's a paper on it too w
>> ah, nostalgia
Ah, "mantissa!" Haven't heard "mantissa" in decades...
Is there such a thing as a "praying mantissa?" Seems like there could be a good
geek joke about it.
JPK
> However all procedures I have seen use a division of 4, which is quite
> puzzling to me. A real data file co
I saw explicitly that it is not limited to EU.
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
++
>>That said, model phases are not so bad. In fact, in all my experiments with
>>fake data the model-phased 2mFo-DFc map always has the best correlation to
>>the "true" map. If you substitute the "true" phases and use the 2mFo-DFc
>>coefficients you actually make things worse. Counter-intuitive
6) I most sincerely hope that, if I stick to my five New Year’s resolutions
and stop wasting the cryo-EM community’s time, my fellow Canadians will not
extradite me to the fake-news country at our southern border.
I know this is a joke, but we in the USA are not a fake news people, and plea
>>I feel you went ahead with right strategy.
I agree with this part regarding lowering symmetry.
>>For 2.1 A datasrt, the appropriate drop in Rfree/ Rwork is a strong
>>indicator, i believe.
This is not true—even non-twinned data will improve in R values with twinning
operators added as parame
Doesn’t the phrase “each-and-every single photon counting capability” imply
that quantum efficiency is 100%? I don’t think this is possible—what is the
quantum efficiency of these detectors?
JPK
+
Jacob Pearson Keller
Research Scientist / Looger L
ensure such a mistake does not occur in the future.
From: Marcus Winter
Sent: Wednesday, January 16, 2019 11:25 AM
To: Keller, Jacob ; CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] hybrid photon counter in the home lab
Dear Jacob,
Thank you for your reply. You’re correct, of course. As shown below
Shouldn’t it be possible to look at the ratio of peak heights of O’s versus S
or P to figure out which is more likely? The must be thousands of examples in
the pdb with which to determine the ratio, even if one restricts the analysis
to “high resolution” structures.
JPK
+++
reply to this message and follow with
its deletion, so that we can ensure such a mistake does not occur in the future.
From: Eleanor Dodson
Sent: Sunday, February 17, 2019 6:12 PM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] SO4 or PO4
Well - I try to quantify the relative
this message and follow with
its deletion, so that we can ensure such a mistake does not occur in the future.
From: Goldman, Adrian
Sent: Sunday, February 17, 2019 10:48 PM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] SO4 or PO4
The total number of electrons in the two
Keller
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+
The content of this email is
It's a crystal with a very large lattice.
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+++
Is that 4+ an April fools’ joke? Pretty crazy if not…can’t think of another ion
with such a charge, well except things like DNA and proteins, but not single
atoms.
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Ca
***
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu>
(214) 6
Hi Reza,
What about seeing whether RNAse and DNAse incubations kill the complex?
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
How about radiation-damaged/smashed Sulphur? You could test this by refining
occupancy of the cys S.
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
11. Crystallography has gleaned a lot of information from relatively poor SNR
imaging. How can these ingenious and robust modelling approaches developed and
applied in crystallography be extended to all forms of imaging, even beyond
cryo-EM--things like EM connectomes, super-res, or even functio
I like both of these points! I would comment/add the following:
1) What are the tools we can use for metals in structural biology? Note, I am
biased here.
-Including validation of solute ions like Na/K/Cl etc
-Some metric of identity confidence?
2) Micro electron diffraction methods - ability t
I don’t think anyone mentioned contacting the authors first—doesn’t this seem
like the first thing one should do?
Jacob
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571
How about a couple more:
-twining and tNCS
-diffuse scattering
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+
This is the old question of what a structural model represents. One perspective
is that it represents the things one is certain about above some threshold,
from the crystallographic data and maps alone. The other perspective is that it
represents the most likely guess of what is actually there.
What about developing a theory of how crystallization happens, i.e., what does
the microscopic “picture” look like when crystals are forming, then predicting
based on that picture? I remember looking into these things about ten years
ago, and there were some cool things being done with various s
Yes, imagine 1 hr, tabletop, unlimited-length, error-free, dirt-cheap gene
synthesis! (With a parallized option for 96-well plates, of course...)
We'll probably just have to wait 10 years.
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
>>It would seem to me that an important issue is also: do get all information
>>out of our diffraction data? By integrating the Bragg peaks we usually
>>neglect the diffuse scattering that could potentially contain additional
>>(dynamic) structural information. This can be cloudy diffuse scatter
Dear Crystallographers,
It seems to be a usual assumption that anomalous scattering is essentially
angularly-independent, e.g.:
http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm
But why the can't we see anomalous-only spots at e.g. 1 Ang resolution in a 2
Ang data set?
This actually has some r
Why do you think you are rejecting anomalous data? What do the normal
tell-tales reveal, like anom CC?
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x31
I don't understand what you are trying to do-are you trying to show, by the
difference in ITC response, that the predictions you made about the
oligomerization are true?
JPK
+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Resea
And yet halides--even iodide--permeate those same lysozyme crystals and
others entirely in <30--60 sec.
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard
Rupp
Sent: Friday, June 27, 2014 9:00 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: R
I have wanted for some time to search for catalytic-triad-like configurations
by defining three Ca-Cb bonds from known catalytic triads, then searching the
pdb for matches, but have not thought of a quick and/or easy way to do
this--can your software do this sort of thing, or is there some other
I think the ref below may be exactly what I am looking for--thanks everyone for
your help. Even when the tips were not exactly what I needed, I learned about
many tools out there which I may use some day. Generally, I am always impressed
by the collegiality and readiness-to-help of all of those
>… I manually attempted chlorine but the density said no.
How did the density say no? Too much, too little…? I guess the bonds are too
short anyway.
What about anomalous signal using the awesomely-sensitive LLG maps from Phaser?
Depending of course on resolution, Cl- can be quite visible, if orde
appreciated, and preferably it would be
without going into a glove box.
Jacob Keller
***
Jacob Pearson Keller, PhD
Looger Lab/HHMI Janelia Farms Research Campus
19700 Helix Dr, Ashburn, VA 20147
email: kell...@janelia.hhmi.org
***
Anyone ever tried a glob of paratone-n for this? I remember it being good for
keeping crystals happy during Xe derivatization, but that was for a relatively
short time. If this is at the synchrotron, the dataset would only take a few
minutes at most, so maybe it would work.
JPK
-Original M
How about merging multiple crystals together a la Wayne Hendrickson's most
recent papers?
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz
Shaanan
Sent: Sunday, July 27, 2014 6:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Heavy A
A somewhat similar question, with a quick answer I hope: when programs output
CC's of 1/2 datasets, are several random halvings compared/averaged, and if
not, does this make a difference, or are the scores so similar there's no point?
JPK
-Original Message-
From: CCP4 bulletin board [ma
Aren't the many chromatographies out there sufficient? Or ultrafiltration? Can
you be a bit more specific about your needs?
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Reza
Khayat
Sent: Tuesday, August 19, 2014 9:55 AM
To: CCP4BB@JISCMAI
I’ve chuckled at the “polish” nomenclature before, as I assumed this was a
reference to certain software developers, but if so, shouldn’t it be “Polish?”
Or does it mean polish, in the sense of shoe polish?
JPK
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry
Powell
>That is, the optimum noise filter is generally the same shape as the signal of
>interest ...
Has this been proven, or it just common sense? And if the filter is the same
shape as the signal, why does one need the signal at all? I guess I don't know
precisely what you mean, but anyway, I like t
Can you do this for structural biology?
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William
G. Scott
Sent: Wednesday, September 03, 2014 2:07 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] paper
On Sep 2, 2014, at 9:10 PM, Avisek Mond
Since you mentioned EtOH, why not do this:
-Make a tray with the appropriate mother liquors
-Make a drop for each well containing mother liquor and high-concentration
ligand in EtOH (you could vary the ratios here as needed.)
-Equilibrate by vapor diffusion until EtOH all goes into the well soln
>I would call everything else 'tabloid science'.
...which might be suitable for some journals?
JPK
Cheers,
Tim
On 10/24/2014 04:11 PM, Michal Jamroz wrote:
> Dnia 2014-10-22, o godz. 15:43:18
> Tommi Kajander napisał(a):
>
>> Would anyone know a software to model (just with some kind of r
Dear Crystallographers,
I thought that for reliable values for Rfree, one needs only to satisfy
counting statistics, and therefore using at most a couple thousand reflections
should always be sufficient. Almost always, however, some seemingly-arbitrary
percentage of reflections is used, say 5%.
Agree with all of this—but how does it reflect on the original question of
whether to use a percent or an absolute number?
JPK
From: Pavel Afonine [mailto:pafon...@gmail.com]
Sent: Friday, November 21, 2014 11:02 AM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Free
Right about the 1000 in that case, but also Rfree with 5% would be
statistically poor. I guess one would be stuck in that case.
JPK
From: Pavel Afonine [mailto:pafon...@gmail.com]
Sent: Friday, November 21, 2014 11:16 AM
To: Keller, Jacob
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Free
>We just had a chance to read this most interesting discussion. We would agree
with Ian that jiggling or SA refinement may not be needed if refinement can in
fact be run to convergence. However, this will be difficult to achieve for large
structures, especially when only moderate to low resolution
Consider this one: Newton's Philosophiæ Naturalis Principia Mathematica. I
think it may have all the relevant terms? I've always liked to think of
scientists more as natural philosophers, although I think there should be
something with a connotation of "art" in there as well, since we do some of
This is where it’s customary to include a small image or two (or better, a link
thereto) which shows the density, and the masters here can tell you there best
guesses—seems to be a bit of a parlour game. Also include info on what is in
the crystallization condition and protein buffer if you dare
What do the twinning tests show? Those space groups can be suspicious, I
believe.
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of RHYS
GRINTER
Sent: Tuesday, December 16, 2014 4:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] P31 or P32
Hi
I would say try to get better crystals and data, and also do a MAD experiment.
But...perfect twins are really hard, I think. Maybe vary the crystallization
conditions a bit, additive screen, seeding, etc.
JPK
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
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