Is it true that HKL adopts the naming convention of putting the screw axes
first and then naming abc if possible, whereas CCP4 just makes the cell
abc? E.g., would HKL ever output by default a p22121 dataset, or would it
automatically be p21212?
JPK
On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
affected is quite small, of course.
Phil Jeffrey
Princeton
On 5/7/12 4:48 PM, Jacob Keller wrote:
Is it true that HKL adopts the naming convention of putting the screw
axes first and then naming abc if possible, whereas CCP4 just makes
the cell abc? E.g., would HKL ever output
I have wondered for a long time now why it is not standard practice for all
crystallization protein stocks to contain either Br- or I- ions instead of
Cl-, even for cationic buffers like TRIS, which could be titrated with HBr
or HI to get in the 10+ mM range. Also, one could use Cs or Rb for the
Why not run a number of jobs in parallel with varying numbers of
monomers/asu?
JPK
On Mon, Apr 30, 2012 at 4:20 PM, mjvdwo...@netscape.net wrote:
Provided that you guess the number of copies and your guess is reasonably
close, my experience is that Phaser will do the job. But you have to tell
Wouldn't the lack of solubility of the alpha form of DDM suggest an easy
purification protocol for the beta form?
JPK
On Fri, Apr 27, 2012 at 8:40 AM, R. M. Garavito rmgarav...@gmail.comwrote:
Hongjun,
I am in agreement with Bert as DDM is exceedingly difficult to
crystallize, even in
Those don't look like DDM crystals I've seen, but the diffraction pattern
does not look much like protein diffraction either. Which things from the
picture did you shoot--the rods/needles?
Jacob
On Fri, Apr 27, 2012 at 5:07 AM, 于洪军 hongju...@moon.ibp.ac.cn wrote:
Hi,
I am trying to screen
I had heard that there was a world-wide Tungsten shortage, but this is
ridiculous!
JPK
On Wed, Apr 25, 2012 at 1:29 PM, H. Raaijmakers hraaijmak...@xs4all.nlwrote:
That's nothing. Once someone wrote me because the tungsten atom of my
Tungsten containing formate dehydrogenase had dissapeared.
Where can one find a discussion of the differences between Aimless and
Scala?
JPK
On Mon, Apr 16, 2012 at 8:28 AM, Harry Powell ha...@mrc-lmb.cam.ac.ukwrote:
Dear all
We are pleased to announce the public release of new versions of iMosflm
and Mosflm. We have addressed many bugs and
I look forward to hearing from others how best to handle this in
refinement.
Dose-dependent occupancies (tau of an exponential decay function?) refined
against unmerged data
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist
Dear CCP4BB,
due to increasing demand, it seems we should put together a workshop on
data fabrication, covering the various important topics (chaired by JHo):
--Images: the future of fabrication? How long can we rely on database
Luddism?
--Ways out: how to leave a trail of accidental data
hat is off to them.
Best regards,
Jim
On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
Dear CCP4BB,
due to increasing demand, it seems we should put together a workshop on
data
fabrication, covering the various important topics (chaired by JHo
,
Jim
On Mon, Apr 2, 2012 at 8:15 AM, Jacob Keller
j-kell...@fsm.northwestern.edu wrote:
Dear CCP4BB,
due to increasing demand, it seems we should put together a workshop
on data
fabrication, covering the various important topics (chaired by JHo):
--Images: the future
I like your point--somehow we should enlist the evil inclination to power
our science, a la Faust. How is it that those hackers are so innovative for
so little reward? I remember a Smithsonian article years ago which quoted
the calculated mean $/hr rate of money counterfeiters as being
What's the harm? Seems relevant to crystallographers, and not for
self-promotion, but just to help, share an interesting tip. Perhaps you can
think of it as a response to an un-asked but plausible question, i.e., how
can I treat my coverslips to make them more receptive to organic
Dear Crystallographers,
it occurred to me that most datasets, at least certainly since the advent
of synchrotrons, have probably some degree of radiation damage, if not some
huge degree thereof. Therefore, I was thinking an exposure-dependent
parameter might be introduced into the atomic models,
Of
*Jacob
Keller
*Sent:* Monday, March 19, 2012 7:46 AM
*To:* CCP4BB@JISCMAIL.AC.UK
*Subject:* [ccp4bb] Refining Against Reflections?
** **
Dear Crystallographers,
** **
it occurred to me that most datasets, at least certainly since the advent
of synchrotrons, have probably some
Switch ethanol in the stain. Also, there was talk a while ago about making
your own instant blue stains--it works like bradford reagent, I think.
Perhaps look back at previous postings?
JPK
On Thu, Mar 15, 2012 at 9:24 AM, Thomas Edwards t.a.edwa...@leeds.ac.ukwrote:
Dear BB,
Apologies for
Hey, that was my post! NB this cannot be used for native gels, I don't
think.
Jacob
On Thu, Mar 15, 2012 at 9:47 AM, Cécile Breyton cecile.brey...@ibs.frwrote:
Hi Ed,
A few years back there has been a thread on copper staining that leads to
negative staining, but works well, is very fast
On Thu, Mar 15, 2012 at 11:14 AM, Jon Agirre jon.agi...@gmail.com wrote:
The best reproduction I can suggest would be to setup one or two LCP
experiments exchanging the protein for its buffer. If you get crystals, you
know for sure they're not protein.
It should be pointed out that the
(*) ADP = Atomic Displacement Parameters
But aren't *isotropic* b-factors subsumed under this TLA (three-letter
acronym?)
JPK
On Fri, Mar 2, 2012 at 11:38 AM, Ian Tickle ianj...@gmail.com wrote:
(*) ADP = Atomic Displacement Parameters
or anisotropic displacement parameters?
See
Can't there be a group of atoms?
JPK
On Fri, Mar 2, 2012 at 12:00 PM, Ian Tickle ianj...@gmail.com wrote:
I'm aware of this document. Personally I prefer ADP = Atomic
Displacement
Parameters over anything ele, because, given that Atomic Displacement
Parameters can be parameterized in
Is the direction of rotation correct? I got some data that were going
the wrong way once.
JPK
Hey, it could be that you just have a big oligomer--any support for
that in the relevant literature? A 10-mer would probably beat out an
s200, no? Do you have any other way to ascertain the oligomeric state?
Jacob
On Tue, Feb 21, 2012 at 5:21 PM, Raji Edayathumangalam
r...@brandeis.edu wrote:
You can also try putting a different affinity tag on the other
terminus, and use that as a second step.
JPK
On Wed, Feb 15, 2012 at 11:25 AM, Xiaodi Yu uppsala@hotmail.com wrote:
Hi Sivasankar:
Are you sure it is due to the protein degradation? Maybe you can try to do a
western blot or
Are there any all-D proteins out there, of known structure or
otherwise? If so, do enantiomer-specific catalyses become inverted?
JPK
On Wed, Feb 15, 2012 at 8:05 AM, David Schuller dj...@cornell.edu wrote:
Wukovitz Yeates (1995) Nature Struc. Biol. 2(12): 1062-1067
predicts that the most
isomerase or set of
isomerases of appropriate properties, this could be helpful for
getting the culture started--or even for preying on the L world?
On Wed, Feb 15, 2012 at 12:17 PM, David Schuller dj...@cornell.edu wrote:
On 02/15/12 12:41, Jacob Keller wrote:
Are there any all-D proteins out
Dear Crystallographers,
thanks for all of the responses and conversation. I have culled
together the various references which have been sent on the BB and
which I have come up with, and posted them below. Worthy of special
mention, I think, is the first one (Lange et al), in which 46 (!)
Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
On Feb 15, 2012, at 18:08, Jacob Keller j-kell...@fsm.northwestern.edu
wrote:
I would say the better practice would be to collect higher
multiplicity
15, 2012, at 10:28 AM, Jacob Keller wrote:
So who out there wants to start an all-D microbial culture by total
synthesis, a la the bacterium with the synthetic genome a while back?
Could it work, I wonder? I guess that would be a certain benchmark for
Man's conquest of nature.
JPK
ps maybe
Dear Crystallographers,
I am looking for references which discuss the validity of the
assertion that multiple crystal structures of the same or similar
proteins can be considered freeze-frame snapshots of actual
conformations assumed in solution. In a way, the assertion seems
almost definitely
How could they not be snapshots of conformations adopted in solution?
Let me clarify--sorry about that. Consider several structures of the
same protein solved under different conditions, or several homologs
solved under similar conditions, or both. Further, let's say some
structural element,
Interesting to juxtapose these two responses:
James Stroud:
How could they not be snapshots of conformations adopted in solution?
David Schuller:
How could that possibly be the case when any structure is an average of all
the unit cells of the crystal over the timespan of the diffraction
Isn't calcium-calmodulin one of the archetypical examples of the
crystal structure probably not representing the solution structure
(perhaps because the crystallization pH = 4.5)? Look at that linker
helix--how stable can that be in solution? I don't think a single one
of the NMR ca-calmodulin
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
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
Well, perhaps it is because size exclusion chromatography is used so
little in the life sciences؟, and who really cares how it works
anyway?؟
JPK
On Tue, Feb 7, 2012 at 3:18 PM, Matthew Franklin mfrank...@nysbc.org wrote:
On 2/7/12 4:02 PM, Jacob Keller wrote:
Dear CCP4BB,
this is perhaps
Sad was the day when I mounted this puppy and it shot to 8-10A. Room
temperature. And messing around with cryos didn't help either.
But if that puppy had been smaller, it might have diffracted even
worse, and just think if that little icy crystal had been bigger...
JPK
Can't remember the
in reciprocal
space should perhaps be an ellipsoid, not a sphere. I know there are
several programs for anisotropic scaling, but I'm not aware of any
that apply anisotropic resolution cutoffs (or even whether this would
be advisable).
Cheers
-- Ian
On 27 January 2012 17:47, Jacob
space should perhaps be an ellipsoid, not a sphere. I know there are
several programs for anisotropic scaling, but I'm not aware of any
that apply anisotropic resolution cutoffs (or even whether this would
be advisable).
Cheers
-- Ian
On 27 January 2012 17:47, Jacob Keller j
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
j-kell...@fsm.northwestern.edu wrote:
Dear Crystallographers,
I cannot think why any of the various flavors of Rmerge
Can't you get a plug-in for that?
JPK
On Thu, Jan 26, 2012 at 11:35 AM, Dale Tronrud
det...@uoxray.uoregon.edu 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
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
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 do
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 jjhe...@lbl.gov 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
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 stacy.biot...@gmail.com wrote:
Dear All,
I am working on plant proteins and solved a structure, there is an extra
density which
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
katherine.sip...@gmail.com wrote:
Hi Rashmi,
In my experience native (even blue native) on proteins
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 is
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 dbon...@ihv.umaryland.edu wrote:
Isn't it true that we cannot even agree on what MAD stands for?
Is the following right?
M =
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
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,
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
, 2012 at 12:33 PM, Dale Tronrud
det...@uoxray.uoregon.edu 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 molecular
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 pat.l...@drexel.edu wrote:
Does anyone have any experience with formation of crystals of dodecyl
maltoside in the presence of
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 gradual nature of the
lattice effect, but it is not exactly what I am looking for. I am
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
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
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 epozh...@umaryland.edu wrote:
On Mon, 2012-01-09 at 10:28 +, Guillaume Gotthard wrote:
Is there a mean to
The word theory in this thread/question has to be clarified better.
Jacob
On Mon, Jan 9, 2012 at 1:27 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hi,
in my opinion the resolution limit of crystals from large complexes/
membrane proteins is
/
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 j-kell...@fsm.northwestern.edu
wrote:
Actually, as a way to make this type of figure, I think there are
programs which output simulated diffraction
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
j-kell...@fsm.northwestern.edu wrote
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 ustcwebri...@gmail.com wrote:
Dear all,
I recently collected a dataset (~2000 frames) from a single crystal.
If merge first 600 frames
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:
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
mjvanra...@cnb.csic.es wrote:
reminds me of these
Can you clarify your reason for doing this?
JPK
On Mon, Dec 12, 2011 at 3:36 PM, Fred ccp4bb.l...@gmail.com 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
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
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 strongly
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 has been
thoroughly, clearly, and authoritatively discredited as a data
evaluation metric
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 Keller wrote:
Let me refine my question (sorry for my lack of clarity
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
Just you wait--he'll be back...won't he?
On Tue, Nov 29, 2011 at 11:11 PM, James Stroud xtald...@gmail.com 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
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
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
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
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
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
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
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,
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 rsanishv...@anl.gov wrote:
Depending on the crystal shape, “random orientation” is not
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
with 180 and one with 360 frames, each from different but similar
crystals--see below. I can't
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 c...@ysbl.york.ac.uk wrote:
Yes - I have seen something similar at a
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
--
How about Phaser with partial MR structure?
JPK
On Tue, Nov 15, 2011 at 3:56 PM, Feng Guo fengg...@gmail.com 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
Hmm, works fine for me. Maybe disable user account control?
Jacob
On Thu, Nov 3, 2011 at 7:54 AM, Jan Dohnalek dohnalek...@gmail.com wrote:
does not seem to create anything runnable - please any experience here?
I downloaded the latest Windows package all users - type. Installed under
admin
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
katherine.sip...@gmail.com wrote:
Hi all,
I'm going to interject into the middle of this rousing though protracted
debate to pick
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 Keller
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
***
. But unless I read 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 j-kell...@fsm.northwestern.edu wrote:
Dear Crystallographers,
I am sending this to try to start a thread
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,
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob Keller
[j-kell...@fsm.northwestern.edu]
Sent: Friday, October 28, 2011 5:05 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] raw data deposition
What about a case in which two investigators have
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,
Gerard.
--
On Thu, Oct 27, 2011 at 11:30:20AM -0500, Jacob Keller wrote
, Jacob Keller j-kell...@fsm.northwestern.edu 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 pics). Has
anyone seen this before? Is it some effect of the refinement
over-fitting
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
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
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
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
frank.vonde...@sgc.ox.ac.uk wrote:
Cool - we've found our volunteer!!
On 26/10/2011 17:28, Jacob Keller wrote:
Is anyone seriously questioning whether we should archive
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
, if 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 epozh...@umaryland.edu 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
--
I'd jump
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
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