better in pharma every day...
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
Dear Crystallographers,
are there any additional problems or known issues running ccp4 or
other xtal software on windows 7 (beyond those of Vista, etc.?) Your
input would be really appreciate before I sink my own personal $$$
into a new laptop
Jacob Keller
Dear Crystallographers,
once again I am filled with graditude to this list--there were many
helpful responses and even some geek humor. I have decided to go with
a dual-boot windows7/linux, which seems easy enough. All the best, and
thanks everyone for your quick and helpful advice.
Jacob Keller
somehow "swamping
out" the other signal? Perhaps the phases are tainted by the presence
of semet in the model?
Looking for suggestions,
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
double your signal for SeMet and start seeing
> sulfurs.
> An alternative explanation, you've blasted your crystals at the synchrotron
> and the remaining anomalous signal is too weak to show the sulfurs.
> Just two thoughts,
> Jürgen
> On Sep 1, 2011, at 4:03 PM, Jacob Keller
Well, I guess I have always been curious what is the gold standard
here--perhaps SEC, ITC, SPR, pulldowns? What if SEC shows a
polydisperse sample with weak oligomerization, or SPR a very weak
binding constant? Do we then revert to a functional assay? Or what if
the functional assay does not show a
mea culpa! How about FRET?
JPK
On Mon, Sep 5, 2011 at 11:39 AM, Bosch, Juergen wrote:
> Hi Jacob,
> you forgot cross-linking to stabilize a weak complex and verify that it
> exists.
> Jürgen
> On Sep 5, 2011, at 11:45 AM, Jacob Keller wrote:
>
> Well, I guess I have always
NMR...take that!
JPK
2011/9/5 Andreas Förster :
> AUC !
>
>
> Andreas
>
>
>
> On 05/09/2011 6:00, Jacob Keller wrote:
>>
>> mea culpa! How about FRET?
>>
>> JPK
>>
>> On Mon, Sep 5, 2011 at 11:39 AM, Bosch, Juergen wrote:
>&g
at mednet dot ucla dot edu
> http://labs.pharmacology.ucla.edu/huanglab/
>
>
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller
> [j-kell...@fsm.northwestern.edu]
> Sent: Monday, September 05, 2011 10:10 AM
> To: CCP4BB@JI
ecular & Medical Pharmacology
>> 310-825-4329
>> jinghuang at mednet dot ucla dot edu
>> http://labs.pharmacology.ucla.edu/huanglab/
>>
>>
>> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob Keller
>
conversion to another file without problems...
Jacob Keller
#CCP4I VERSION CCP4Interface 2.1.0
#CCP4I SCRIPT LOG import
#CCP4I DATE 06 Sep 2011 16:29:11
#CCP4I USER 'UNKNOWN'
#CCP4I PROJECT 3mgl
#CCP4I JOB_ID 3
#CCP4I SCRATCH C:/Ccp4Temp
#CCP4I HOSTNAME chloe
#CCP4
(or whatever ), restart ccp4i, and voila it works!
>
> So sorry, this looks like a cock-up in the windows distribution :(
>
> HTH
> Martyn
>
> On Tue, 2011-09-06 at 16:34 -0500, Jacob Keller wrote:
>> Dear Crystallographers,
>>
>> in trying to convert a mmcif
Is there a CNS BB?
JPK
On Thu, Sep 8, 2011 at 2:20 PM, Laurie Betts wrote:
> Sorry - I already belong to 2 bbs and to add another would make me really a
> mess.
>
> Can someone out there who is a CNS developer please send me an email off
> this bb I need to ask a glibc question.
>
> Thanks, Laur
I have noticed, in new versions of OSes, that there generally is
rampant violation of the concept of "if it ain't broken, don't fix."
Shouldn't there be more moments of delight, when you see they have
solved a previous poorly-engineered feature with an elegant solution?
But a lot of the time, you h
ation from a theoretical null hypothesis? Seems
like this could be done, but I have never seen this in the
literature...
Best,
Jacob Keller
--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j
>> Maybe one should do a gradient of
>> gluteraldehyde concentrations, then plot the deviation of the observed
>> cross-linked oligomerization from a theoretical null hypothesis?
>
> Right - just do it side-by-side with a protein known to be monomeric of
> roughly the same size/lysine content... A
I think I know another protein that does this: gelatin! (Well, not the
crystallization part...)
Jacob
On Fri, Sep 16, 2011 at 2:41 PM, Phoebe Rice wrote:
> Gamma delta resolvase catalytic domain stock solutions used to make a nice
> clear jelly at 4 degrees, but it was perfectly reversible by w
Why not ask the authors for a reprint?
JPK
On Wed, Sep 21, 2011 at 10:49 AM, anna delprato wrote:
> Hello All,
> I apologize in advance for the off topic subject but does anyone out there
> have access to a journal called Anticancer Agents Med Chem ? I am having
> difficulty obtaining this artic
Wow, neutrons are pretty cool! No radiation damage--and time
resolution? I guess this is since they have much higher energy, and
are measurable individually? What are the numbers for fluxes
(neutrons/sec)? Are the neutrons all at one energy, or is there a
bandwidth?
JPK
> With X-rays, Laue diffra
.
> Q Rev Biophys. 1995 May;28(2):171-93.
>
> best wishes
>
> James
>
> --
> Dr. James W. Murray
> David Phillips Research Fellow
> Division of Molecular Biosciences
> Imperial College, LONDON
> Tel: +44 (0)20 759 48895
> _______
That value, 2200m/s, is pretty slow--there are some bullets that go
faster than that, I think...
JPK
On Fri, Sep 23, 2011 at 11:59 AM, Andreas Ostermann
wrote:
> Jacob Keller wrote:
>> Wow, neutrons are pretty cool! No radiation damage--and time
>> resolution? I guess this is
I don't really get your question: assuming the sigmas you mentioned
are in an anomalous map and therefore have been located, why don't you
just plug it into your usual phasing algorithm?
Jacob
On Fri, Sep 23, 2011 at 1:49 PM, Yuri Pompeu wrote:
> Hello everyone,
> I have a data set >99% complete
I vaguely recall notepad doing something wacky with files in certain
cases...why don't you get the excellent text editor NoteTab Light
[sic] (I use it all the time--free and works great), then take a look
at your files and see whether MS notepad altered the files.
JPK
On Mon, Sep 26, 2011 at 2:42
what I'm doing:
>> >
>> > 1) superpose proteinA.pdb onto proteinB.pdb : works, but gives out
>> > proteinA_lsq1.pdb with extra empty lines (not the anisou lines ;o) )
>> >
>> > 2) superpose proteinA_lsq1.pdb onto proteinC.pdb : doesnt work because
interpret, making what would seem to be a simple task take much
longer...
Jacob Keller
--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
***
I actually looked at an EtBr MSDS a while ago, and was shocked at how
benign it was. I also heard from someone that they used to feed it to
Argentinian cows routinely a few years back...
JPK
On Sat, Oct 1, 2011 at 1:56 AM, James Stroud wrote:
> If you can reproduce the crystals and have the mate
>> There exists a less toxic chemical than EtBr to stain DNA: SYBR safe
>> DNA stain (a fluorescence dye sold by a certain vendor).
>
> SYBR Safe is about 10X less sensitive though.
Can you do the toothbrush test with SYBR Safe?
JPK
***
Jacob Pearson Kell
range. Does anyone have a clever way of getting bicarb into these
crystals? Grow them under CO2? Transfer them to higher pH, and hope
for the best?
Jacob Keller
Why not just go to P1, then build up the symmetry? Is completeness low?
JPK
On Mon, Oct 3, 2011 at 10:14 AM, Eleanor Dodson wrote:
> Further Qs.
>
> Do you have a noncryst translation parallel to the b axis (ctruncate will
> list any such translation..)
>
> If the b shift is 0.5 then the 0k0 "ab
Dear Crystallographers,
I cannot get BLAST to find all proteins with the motif cxcxcxc or at
least cxcxc. It seems to think of "x" as an actual amino acid rather
than a wildcard. There must be some easy way to do this? Ordinarily to
find a short motif, I would just paste the sequence and get the
a
===
> http://manchester.academia.edu/DavidBriggs (v.sensible)
> http://xtaldave.wordpress.com/ (sensible)
> http://xtaldave.posterous.com/ (less sensible)
> Twitter: @xtaldave
> Skype: DocDCB
>
>
>
> On 4 October 2011 21:34, Jacob Keller
> w
CVCVCVCLCVCVCLCVCLCVCLCVCVCVCVCLCVCLCVCLCVCVCVCVCLLCMSLCMCMCMCMCMCMCMCMCMSLCMSLCMCMCMCMCMCMCICMCMCICICMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCIIEGNK
Maybe it's just a sequencing glitch?
JPK
On Tue, Oct 4, 2011 at 4:05 PM, Jacob Keller
wrote:
> Thanks everybody, I tried using
>
> --toolkit tuebingen mpi
> --Scanprosite
>
>
> Maybe it's just a sequencing glitch?
Not so--BLAST showed there are a whole cadre of these things in
various genomes. Go figure.
JPK
>
> JPK
>
>
> On Tue, Oct 4, 2011 at 4:05 PM, Jacob Keller
> wrote:
>> Thanks everybody, I tried using
>>
>&
Dear Crystallographers,
is anyone aware of references studying variation in cell params
systematically as a function of temperature, with many points on the
curve (not just RT and 100K?)
Jacob Keller
--
***
Jacob Pearson Keller
Northwestern University
Dear CCP4ers,
I am trying to run watertidy from the windows gui to add waters, but
get the error message below. Since the gui is so short, I don't think
I am missing anything, so what I am doing wrong? Is there an
alternative water-picker in the gui? I used to use watpick, but I
believe that was i
f not this one? There
is of course arp/warp, but not in windows...
Jacob
On Wed, Oct 19, 2011 at 1:32 PM, Ed Pozharski wrote:
> On Wed, 2011-10-19 at 12:45 -0500, Jacob Keller wrote:
>> Is there an
>> alternative water-picker in the gui?
>
> watertidy is not a water-picker
&
Is anyone seriously questioning whether we should archive the images
used for published structures? That amount of space is trivial, could
be implemented just as another link in the PDB website, and would be
really helpful in some cases. One person could set it up in a day! You
could just make it a
Touche! But alas, I have no access to the PDB's server, so...
JPK
On Wed, Oct 26, 2011 at 11:54 AM, Frank von Delft
wrote:
> Cool - we've found our volunteer!!
>
> On 26/10/2011 17:28, Jacob Keller wrote:
>>
>> Is anyone seriously questioning whether we should
One thing that the poll is useful for is something I find surprising:
~40% when I checked found storing images a waste of time. So, I guess
this might be useful for finding the "silent [significant] minority."
Why not have those folks chime in about why they think this is
useless, even to store ima
hould be an extra category of answer that would be
> "I don't care", so that people who have no opinion do not get confused with
> those who have an articulate position against the proposal, and wh should
> then articulate it!
>
>
> With best wishes,
>
>
e: DocDCB
> ====
>
>
>
> On 27 October 2011 17:27, Jacob Keller wrote:
>> Dear Crystallographers,
>>
>> In the course of a reasonably smooth refinement, all of a sudden there
>> is a huge worm-hole-type blob in the electron density (see
Since this hasn't been brought up--there is the consideration that in
10 or more years maybe x-ray crystallography will be completely a
thing of the past, with some kind of massively-superior modality
taking over. Of course there is no way to bank on this, but I am
wondering whether this is somethi
Blob is gone--something funny happened, I guess. I went back to using
the original mtz from scala, removed and replaced a bunch of waters,
and no more worm! I can't really figure it out, and wish I knew
exactly what happened, but I think I am just going to non-chalantly
move along.
Jacob
On Thu,
What about a case in which two investigators have differences about
what cutoff to apply to the data, for example, A thinks that Rsym of
50 should be used regardless of I/sig, and B thinks that I/sig of 2
and Rpim should be used. Usually A would cut off the data at a lower
resolution than B, especi
> E-mail: bshaa...@bgu.ac.il
> 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 Jacob Keller
> [j-kell...@fsm.northwestern.edu
to me that this step would be pretty painless,
as it is merely an extension of the current system--just add a link to
the pulldown menu!
Best Regards,
Jacob Keller
--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***
d the tenor
> of this discussion completely wrongly, opt-in is precisely what is not being
> proposed.
>
> Adrian Goldman
>
> Sent from my iPhone
>
> On 31 Oct 2011, at 18:02, Jacob Keller wrote:
>
>> Dear Crystallographers,
>>
>> I am sending this to tr
Maybe you could refine it using our new-fangled methods to improve the
model? (Couldn't resist such irony!)
Jacob
On Tue, Nov 1, 2011 at 9:34 AM, Katherine Sippel
wrote:
> Hi all,
>
> I'm going to interject into the middle of this rousing though protracted
> debate to pick your brains. I am in p
Dear Crystallographers,
I would like to transfer data from x-files (HKL2000) into scala, and
think that the best way to do it is to tell HKL "no merge original
index." Is that right, or is "no merge include partials" better?
Jacob
--
***
Jacob Pearson Kel
Hmm, works fine for me. Maybe disable user account control?
Jacob
On Thu, Nov 3, 2011 at 7:54 AM, Jan Dohnalek wrote:
> does not seem to create anything "runnable" - please any experience here?
>
> I downloaded the latest Windows package "all users" - type. Installed under
> admin (as it would n
How about Phaser with partial MR structure?
JPK
On Tue, Nov 15, 2011 at 3:56 PM, Feng Guo wrote:
> Hi, there,
>
> Maybe someone asked this question before, but I couldn't find it in the
> archive.
>
> We use the native data to do molecular replacement before, but only part of
> the model fit
Dear Crystallographers,
I have crystals containing 666mM NH4 and 540mM Na, and there appears
to be a "water" which is only about 2.2 Ang from some polar atoms. It
is currently reasonably happy as a Na, but is there any reasonable way
to decide which cation is there?
JPK
--
*
I also have seen similar. I was thinking it was potentially some kind
of radiation damage? Is there a good paper which examines what
chemistries are seen in rad damage?
Jacob
On Thu, Nov 17, 2011 at 5:39 AM, Eleanor Dodson wrote:
> Yes - I have seen something similar at a lower resolution, but v
Dear Crystallographers,
I am getting an error when I try to merge two mtz's from mosflm, one
with 180 and one with 360 frames, each from different but similar
crystals--see below. I can't imagine this really exceeds the max
number of records, so what am I doing wrong? Additionally but related,
wha
Generally speaking, don't we agree that "planned" or "rational" is
better than "random?" (Having trouble understanding the argument for
randomness here...)
Jacob
On Fri, Nov 18, 2011 at 9:40 AM, Sanishvili, Ruslan wrote:
> Depending on the crystal shape, “random orientation” is not always random
you have a 64-bit system with lots of memory (and a 64-bit
> build)
>
> Phil
>
>
>
> On 18 Nov 2011, at 15:36, Jacob Keller wrote:
>
>> Dear Crystallographers,
>>
>> I am getting an error when I try to merge two mtz's from mosflm, one
>> wit
Just to clarify: I think the question is about the mathematical sense
of "significance," and not the functional or physiological
significance, right? If I understand the question correctly, wouldn't
the reasoning be that admittedly each atom in the model has a certain
positional error, but all toge
I am curious how all of this can be more than splitting hairs, i.e.,
under what conditions can this 1Ang domain motion mean something
biologically significant? Proteins are pretty flexible, after all,
especially between domains.
JPK
On Mon, Nov 21, 2011 at 6:41 PM, James Stroud wrote:
> On Nov 2
I understand that absorbed dose increases with presence of heavy
atoms, but I don't understand why that should play a role in damaging
the crystal, as heavy atoms such as in cacodylate should probably
usually not be near enough to protein atoms to cause problems. At
100K, isn't it true that seconda
Not that Phaser needs my approval, but I recently did exactly what
Randy recommended and it really found basically all of the S and Cl
sites, with data at resolution 2.2 Ang and wavelength 0.979 Ang, too.
I also played a bit with the sigma cutoff for adding new sites so that
the stronger sites (Se
Dear Crystallographers,
is there a ccp4 program--or otherwise--which can compute ca-ca
distances of corresponding residues between two superposed structures?
Jacob
--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
emai
Let me refine my question (sorry for my lack of clarity): is there a
program that will output the distances between the corresponding ca's
of a superposition on a residue-by-residue basis, and not just a
global RMSD value (doubtless these numbers are part of the
superposition algorithm itself)? I w
9, 2011 at 3:44 AM, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Jacob,
>
> Coot prints this information to the terminal, so you can start coot and
> 'tee' its output into a file.
>
> Tim
>
> On 11/28/2011 11:53 PM, Jacob Ke
Dear Crystallographers,
does anyone have any nice examples/references of proteins which form
demonstrably physiologically-relevant oligomers in crystals, but which
do not appear to do so in solution? I am thinking particularly that
domains of membrane proteins which oligomerize primarily through t
Just you wait--he'll be back...won't he?
On Tue, Nov 29, 2011 at 11:11 PM, James Stroud wrote:
> With such a nice parting letter, we find it disheartening to let you go.
>
> James
>
> On Nov 29, 2011, at 7:44 PM, debanjan choudhuri wrote:
>
> To whom it may concern,
> I am writing this in reques
Dear Crystallographers,
I hate to broach this subject again due to its wildly controversial
nature, but I was wondering whether there was any reference which
systematically analyses resolution cutoffs as a function of I/sig,
Rmerge, Rmeas, Rpim, etc. I strongly dislike Rmerge/Rcryst for
determinin
Gaudet
EGFR kinase--thanks to Markus Seeliger
FokI nuclease--thanks to Artem Evdokimov
NKR-P1 receptors--thanks to Jan Dohnalek
Insulin--thanks to Eleanor Dodson
All the best,
Jacob Keller
--
***
Jacob Pearson Keller
Northwestern University
Medical
Hi Ethan, thanks for pushing me to clarify--see below.
>> I hate to broach this subject again due to its wildly controversial
>> nature, but I was wondering whether there was any reference which
>> systematically analyses resolution cutoffs as a function of I/sig,
>> Rmerge, Rmeas, Rpim, etc. I st
ust
> proposing more statistically sound alternatives. That is not the same ...
>
> A.
>
>
> On 6 Dec 2011, at 21:44, Ed Pozharski wrote:
>
>> On Tue, 2011-12-06 at 13:43 -0600, Jacob Keller wrote:
>>> The question is: "is there a reference in which Rmerge ha
Can you clarify your reason for doing this?
JPK
On Mon, Dec 12, 2011 at 3:36 PM, Fred wrote:
> Hi James,
> In my first post "arbitrary orientation into the cell" only means not
> parallel to any crystallographic axis, which would simplify things very
> much. I want to apply the 4-fold axis to th
Does anyone know where one can acquire some Penrose tiles? I think
they'd be great toys as well, and drive you a little bonkers. Maybe a
kitchen/bathroom floor made from them?
Jacob
On Tue, Dec 13, 2011 at 5:03 PM, VAN RAAIJ , MARK JOHAN
wrote:
> reminds me of these symmetric 2D P3 lizards:
> ht
Dear Crystallographers,
is there a convention for denoting/measuring pore sizes in protein
structures? Maybe inter-atom distances minus van der Waals radii?
JPK
--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email:
Need more info: how many degrees per frame? Also, on integration, do
various stats change over the 'sets?
JPK
On Wed, Jan 4, 2012 at 7:42 AM, Zhiyi Wei wrote:
> Dear all,
>
> I recently collected a dataset (~2000 frames) from a single crystal.
> If merge first 600 frames (sca1) or last 600 frame
Dear Crystallographers,
has anyone come across a figure showing a normal diffraction image,
and then next to it the equivalent molecular transform, perhaps with
one image as phases and one as amplitudes? Seems like it would be a
very instructional slide to have to explain how crystallography works
the continuous molecular transform. I think
this would amount to the same thing as the molecular transform of the
model itself--am I right?
Does anyone know which software outputs simulated diffraction images?
Jacob
On Fri, Jan 6, 2012 at 10:25 AM, Jacob Keller
wrote:
> Dear Crystallograph
Also R cryst is sometimes used for the same number, I think (of course
there are historical reasons for the different terms, but...).
JPK
On Mon, Jan 9, 2012 at 8:47 AM, Ed Pozharski wrote:
> On Mon, 2012-01-09 at 10:28 +, Guillaume Gotthard wrote:
>> Is there a mean to obtain statistics abo
The word "theory" in this thread/question has to be clarified better.
Jacob
On Mon, Jan 9, 2012 at 1:27 PM, Tim Gruene wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Hi,
>
> in my opinion the resolution limit of crystals from large complexes/
> membrane proteins is more likely due
t; This program is a relative of nearBragg, which Dale already mentioned.
>
> -James Holton
> MAD Scientist
>
> On Jan 6, 2012, at 5:44 PM, Jacob Keller
> wrote:
>
>> Actually, as a way to make this type of figure, I think there are
>> programs which output
from single waves and an atomistic model inside
> the crystal.
> - - What makes you think the pattern from a larger molecule would have a
> more complex pattern?
>
> Cheers,
> Tim
>
> On 01/10/2012 12:13 AM, Jacob Keller wrote:
>> I like that animation a lot, as it shows the
I think once you start getting down to such small crystals, the spots
are not really important, as the pattern starts getting continuous.
Interestingly enough, I guess for single-molecule diffraction,
resolution is limited only by radiation damage, and not by any sort of
lattice disorder (or even b
Dear Crystallographers,
it seems to me that on a certain level we are always throwing away
(sort of) about half of our data when we merge Bijvoet pairs--why
shouldn't we keep them separate, since we know that they should be a
little bit different, especially in light of the higher multiplicities
w
What exactly is your question--I saw tons of "crystals" of DDM and
PEGs, I think especially P400, if I recall correctly.
JPK
On Wed, Jan 11, 2012 at 7:12 AM, Patrick Loll wrote:
> Does anyone have any experience with formation of crystals of dodecyl
> maltoside in the presence of PEG?
> Pat
>
>
No, I meant the non-lattice-convoluted pattern--the pattern arising
from the Fourier-transformed electron density map--which would
necessarily become more complicated with larger molecular size, as
there is more information to encode. I think this will manifest in
what James H called a smaller "gra
, 2012 at 12:33 PM, Dale Tronrud
wrote:
>
>
> On 01/13/12 09:53, Jacob Keller wrote:
>> No, I meant the non-lattice-convoluted pattern--the pattern arising
>> from the Fourier-transformed electron density map--which would
>> necessarily become more complicated with larger
> By the way, I wouldn't use "MAD" to describe the mergeing of non-isomorphous
> datasets. Strictly speaking, MAD is at least an attempt to measure both
> anomalous (f") and dispersive (f') differences, and I don't think it is
> appropriate to use the term "MAD" when you know the dispersive signal
That is excellent! You refer obviously to the multiple anomalous
discussions on the bb? (Maybe d = disagreement?)
JPK
On Wed, Jan 18, 2012 at 11:42 AM, D Bonsor wrote:
> Isn't it true that we cannot even agree on what MAD stands for?
>
> Is the following right?
>
> M = Multiple-wavelength. I thi
> Can I be dogmatic about this ?
I wish you could, but I don't think so, because even though those
sources call it that, others don't. I agree with your thinking, but
usage is usage.
> a SAD experiment is a single wavelength experiment where you are using the
> anomalous/dispersive signals for ph
This begs the question* whether you want the lemmings to understand
you. One theory of language, gotten more or less from Strunk and
White's Elements of Style, is that the most important feature of
language is its transparency to the underlying thoughts. Bad language
breaks the transparency, remind
Who says this is on a twofold? Also, it would be very helpful to know
what was in the crystallization condition.
JPK
On Thu, Jan 19, 2012 at 12:44 AM, stacy William wrote:
> Dear All,
> I am working on plant proteins and solved a structure, there is an extra
> density which i cannot fix . I am
I have actually done this by running a normal PAGE gel without
stacking gel and switching the electrodes, which seemed to work
swimmingly.
JPK
On Thu, Jan 19, 2012 at 9:25 AM, Katherine Sippel
wrote:
> Hi Rashmi,
>
> In my experience native (even blue native) on proteins around that pI is
> sket
A very similar question: how about smaller motifs, such as various
turn types, etc.?
JPK
On Fri, Jan 20, 2012 at 12:37 PM, Jeff Headd wrote:
> Hi Yuri,
>
> I don't know of a cheat-sheet, but I find the "Introduction to Protein
> Structure" book by Branden and Tooze to useful for illustrations of
Inspired by the recent post about "quasispecies:"
I have been bothered recently by the following problem: why do species
of genetic uniformity exist at all (or do they?)? This first came up
when I saw a Nature paper describing live bacteria extracted from a
supposedly 250-million-year-old salt cry
Whoops--I meant to change the subject line, so if you want to reply,
please use this one not to perturb the original post.
JPK
> Inspired by the recent post about "quasispecies:"
>
> I have been bothered recently by the following problem: why do species
> of genetic uniformity exist at all (or d
Can't you get a plug-in for that?
JPK
On Thu, Jan 26, 2012 at 11:35 AM, Dale Tronrud
wrote:
> Unless you have written on the paper using cursive script. Many schools
> in the US have stopped teaching longhand reading/writing so in a generation
> or two many paper records will be undecipherabl
Dear Crystallographers,
I cannot think why any of the various flavors of Rmerge/meas/pim
should be used as a data cutoff and not simply I/sigma--can somebody
make a good argument or point me to a good reference? My thinking is
that signal:noise of >2 is definitely still signal, no matter what the
Clarification: I did not mean I/sigma of 2 per se, I just meant
I/sigma is more directly a measure of signal than R values.
JPK
On Fri, Jan 27, 2012 at 11:47 AM, Jacob Keller
wrote:
> Dear Crystallographers,
>
> I cannot think why any of the various flavors of Rmerge/meas/pim
> sh
o model,
>> > and looked at the difference density for the ligand, using data cut at
>> > 2.5, 2 and 1.5 Ang where the standard metrics strongly suggested there
>> > was only data to 2.5 Ang.
>> >
>> > I have to say that the differences were tiny, well be
inal apo model,
>> > and looked at the difference density for the ligand, using data cut at
>> > 2.5, 2 and 1.5 Ang where the standard metrics strongly suggested there
>> > was only data to 2.5 Ang.
>> >
>> > I have to say that the differences were tin
One last thing--sometimes crystals can be frozen as is, particularly
if you use mitegen mounts and get nearly all of the mother liquor off
the crystals by dabbing the loop on the dry surface next to the drop
several times. So simple it is always worth a try
JPK
On Tue, Feb 7, 2012 at 2:37 AM,
Dear CCP4BB,
this is perhaps my most egregious off-topic post, but can anyone
explain why the following reference is not findable in PubMed? I can
get it from the ACS website, but not on PubMed or elsewhere. The
journal is on PubMed--is it perhaps because it's funded by ExxonMobil?
Very strange...
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