-SAXS stations* running at the same time for students! This is a
unique hands-on opportunity to learn the highly popular technique which couples
size exclusion chromatography to small angle x-ray scattering.
Richard Gillilan
MacCHESS
--
Cornell High energy Synchrotron Source
Ithaca, NY
could also try ShelXle, available
> at http://ewald.ac.chemie.uni-goettingen.de/shelx/eingabe.php.
>
> Best,
> Tim
>
> On 07/14/2014 10:26 PM, Richard Gillilan wrote:
>> I have a pdb file for a non-protein having C 1 2/c symmetry. PyMol can't
>> recognize the
I have a pdb file for a non-protein having C 1 2/c symmetry. PyMol can't
recognize the spacegroup. Can someone recommend software that can apply the
crystallographic symmetry to give the full structure?
Richard Gillilan
MacCHESS
Cornell University
,
You can find information about where to find the archives here:
http://www.ccp4.ac.uk/ccp4bb.php#archives
Best regards,
Folmer
2014-02-19 14:44 GMT+01:00 Cai Qixu
mailto:caiq...@gmail.com>>:
Dear Richard Gillilan,
Where to find the archives of Dec 2003? I can only find the archiv
Scientific: (VISEX) see smb.slac.stanford.edu/news/Visex.pdf (their
listed products seem to be UV-based, but apparently this one is visible.)
Both of these are proprietary commercial products, so it is impossible to know
exactly what they are doing.
Richard Gillilan
MacCHESS
There was an informative discussion on this very topic back in Dec 1-2, 2003 if
you browse the CCP4BB archives.
Richard Gillilan
MacCHESS
On Feb 12, 2014, at 6:43 AM, Cai Qixu wrote:
Dear all,
Does the I/sigmaI in “Table 1” mean for / or ?
Thanks for your answer.
Best wishes,
Qixu Cai
t photobleaches in bright
x-ray beams over time.
Of course there is always cutting thin slivers of the plastic fluorescent sheet
material everyone uses at beamlines. Not sure where they get that.
Richard Gillilan
MacCHESS
On Feb 14, 2014, at 12:18 PM, Scott Classen wrote:
> Hi Ronnie,
>
this?
Richard Gillilan
MacCHESS
Cornell
_______
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Richard
> Gillilan [r...@cornell.edu]
> Sent: Friday, December 14, 2012 5:20 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] archival memory?
>
> This is too funny. My
reepy purposes. Luckily, as a
space mushroom I will have no interest in private momets of Queen Elizabeth's
life, no matter how amusing they might be.
-artem
On Dec 14, 2012 9:20 AM, "Richard Gillilan"
mailto:r...@cornell.edu>> wrote:
This is too funny. My wife's new job i
ipate that you will then have to move them to
>>> something else.
>>>
>>> Instead of spending time working on the 100 year solution you should
>>> spend your time annotating your data so that someone other than you
>>> can figure out what it is. Lack
d, Dec 12, 2012 at 3:02 PM, Richard Gillilan
mailto:r...@cornell.edu>> wrote:
SanDisk advertises a "Memory Vault" disk for archival storage of photos that
they claim will last 100 years.
(note: they do have a scheme for estimating lifetime of the memory, Arrhenius
Eq
ves with Firewire" Tronrud
>
> On 12/12/2012 1:02 PM, Richard Gillilan wrote:
>> SanDisk advertises a "Memory Vault" disk for archival storage of photos that
>> they claim will last 100 years.
>>
>> (note: they do have a scheme for estimating lifetime of
2012 at 3:02 PM, Richard Gillilan
mailto:r...@cornell.edu>> wrote:
SanDisk advertises a "Memory Vault" disk for archival storage of photos that
they claim will last 100 years.
(note: they do have a scheme for estimating lifetime of the memory, Arrhenius
Equation ... inte
Chronolock tab.).
Has anyone here looked into this or seen similar products?
Richard Gillilan
MacCHESS
se or
disclosure of the contents of this message is not permitted and may be unlawful.
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Richard
Gillilan
Sent: Friday, November 30, 2012 5:21 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4b
at once. In fact, I think we gave the
poster an award for that. I don't have my past notes handy to remember, but
could look it up if you're interested.
Richard Gillilan
MacCHESS
On Nov 30, 2012, at 4:19 PM, Sarathy Karunan Partha wrote:
Dear all,
We did some Izit dye stainin
position, contact Dr. Richard Gillilan at
r...@cornell.edu.
Cornell is an equal opportunity, affirmative action educator and employe
at the F2 beamline. If your samples seem to aggregate rapidly after
preparation, or you think you may have a mixture, you may want to investigate
on-site SEC. Fractions can be collected directly into the same 96-well plates
used by the BioSAXS robot.
I you are interested, contact me (Richard Gillila
In theory, there should be a simple way to calculate P(r) directly from the
crystal structure rather than indirectly from the expected scattering curve.
Distribution of pair distances, r^2 weighted. This would remove any ambiguity
about choice of Dmax. ... but I can't think of any of the common
Note: CHESS has multiple postdoc positions open in various areas of x-ray
science. I am posting the BioSAXS ad here, but applicants will automatically be
considered for all the positions.
Job opening: Postdoctoral As
onnection between extent of data in reciprocal space and model features is not
simple.
Richard Gillilan
MacCHESS
LIKE to go ... but would you actually be able to go? I would also be
interested in hearing from any interested potential organizers.
(Please also keep in mind that SAS2012 is in Australia Nov 2012, so that may
make a difference in your travel plans).
Richard Gillilan
chair-elect ACA SAXS SIG
on for
users at F2 station. We have also purchased an AKTA Purifier size-exclusion
chromatography (SEC) system for use at the F2 beamline. If your samples seem to
aggregate rapidly after preparation, or you think you may have a mixture, you
may want to investigate on-site SEC. If you are interested, co
For the record, the amount of disk storage space per unit cost has doubled
every 14 months for the last 30 years. It's an exponential relationship:
www.mkomo.com/cost-per-gigabyte
So data generated at a very high rate today, will be trivial to store in the
near future. That's not to say it is
Jobs and Apple not only deeply shaped my career, but also my son's path as well.
I bought an Apple II+ with my first Summer's earnings as an undergraduate lab
assistant in organic chemistry in the very early 80's. Spent winter break
writing a printer driver in Apple 6502 code so I could plot mol
Hi Jacob, high-pressure cryocrystallography methods may be useful in this case.
I copied your question to Chae Un Kim here at MacCHESS and he forwards this
suggestion:
--
Hi Richard,
I think pressure cryocooling might be useful.
They may want to check th
Listening to Jobs speak recently, I got the distinct impression that the end of
the era of general desktop computers "PC's" may be on the horizon. Of course
that's iPad sales rhetoric, but it may be that the public moves away from
general computers and that surely will have implications for scie
BioSAXS can also tell you if the protein is folded or not, but in either case,
you may want to purify on site since degradation is so fast. Many BioSAXS
beamlines (including ours at MacCHESS) now have SEC systems on site.
Richard Gillilan
MacCHESS
Cornell University
On Aug 19, 2011, at 3:55
enters. Blue ice seen in the far north
however, appears to be purely a light-scattering phenomenon and not a result of
trapped electrons.
Richard Gillilan
MacCHESS
>
> -James Holton
> MAD Scientist
>
> Todd Geders wrote:
David had developed an empirical theory to model the air, solvent,
Compton & acoustic contributions and correct the integrated data for
these, without background correction of course since the optic DS
background was ultimately to be our data!
...
Hi Ian, did David publish this theory somewhere
Thank you all for your informative responses!
While examining the effects of unusual beam profiles on data
collection due to capillary optics, I had collected a wedge of data
on a large, high-quality lysozyme crystal at 8 different sample to
detector distances. I restricted the analysis of
ff as the square of the distance, the expectation
is that a larger crystal-to-detector distance is better for reduction
of the x-ray background. ..."
Does anyone know of a more rigorous discussion of why background
scatter fades while Bragg reflections remain collimated with distance?
Sorry, I meant to say "does divergence add to the reported mosaicity
value." If so, do actual mosaicity and divergence add in quadrature
to give the reported value?
On Aug 6, 2009, at 6:14 PM, Richard Gillilan wrote:
Does anyone know if beam divergence gets included in the
Does anyone know if beam divergence gets included in the mosaicity
values reported by HKL2000?
(i.e. does it add to the measured divergence (in quadrature)?)
Richard Gillilan
MacCHESS
than pure elements)?
I notice that a number of companies offer XRF standard kits.
Richard Gillilan
MacCHESS
compute the values of I_corr and W ?
-
Thanks
Richard Gillilan
MacCHESS
Some of the error model parameters are defined at the moment by
user, they can be refined iteratively by experimenter by adjusting
parameters in subsequent runs of scalepack, but most of the time it
is not required
ack error model/Bayesian reasoning works? The scalepack manual
has no equations for this.
Richard Gillilan
MacCHESS
Does anyone know of a detailed rigorous discussion of how the
scalepack error model/Bayesian reasoning works? The scalepack manual
has no equations for this.
Richard Gillilan
MacCHESS
oligomeric
state of a protein. Nonetheless, it seems to be a good thing in low
concentrations.
Working at 4C may help.
Richard Gillilan
MacCHESS
On Jul 9, 2009, at 8:57 PM, Susan Tsutakawa wrote:
Hi Bill,
5-10% glycerol usually helps in the majority of cases. However,
some proteins
If I understand the idea correctly, I would still expect to see good
Bragg spots, but the amplitudes would represent the rotationally
averaged protein. This is like the hexagonal water lattice (Ih):
there is "disorder" in how the water molecules are oriented at each
lattice point (not reall
Begin forwarded message:
From: Richard Gillilan
Date: June 23, 2009 9:43:20 AM EDT
To: "Nadir T. Mrabet"
Subject: Re: [ccp4bb] structure <-> function
A very interesting question.
Stephan Jay Gould was well known for his argument that evolution is
contingent on all kinds
Some years ago, I produced a short computer-animated video (complete
with music and narration) for Jon Clardy's group on chorismate
mutase. The e. coli and b. subtilis forms of chorismate mutase
catalyze the same claisen rearrangement but have completely different
folds and hydrogen bond ne
I know that sometimes people like to defocus the x-ray beam at the
sample so that the intensity profile is not sharply peaked. I think
the rationale is that the sharp peak will cause damage, but
contribute few photons to the overall diffraction pattern.
Does anyone know of a reference where
ce is distorted.
Richard Gillilan
MacCHESS
BTW, I've also seen and harvested "ghost crystals" that were bubbles.
Folds of skin can look like crystal edges sometimes.
Speaking of ghosts, I had a dried out drop that looked just like a
statue of Buddha I thought. One of my student
r 5, now maybe 1
micron. Pretty soon no microbeam at all.
I think maybe I'll stick with "small", "smaller than usual", and
someday "extremely small."
I'd love to hear people's opinion on the topic.
Richard Gillilan
MacCHESS
$3M/TB clay tablets
Probably the only medium that will still be practically readable a
few decades from now! Having seen a few up close here on Cornell
campus, I recommend you save the archeologists some headache and bake
them. At least you can write on both sides. The unfortunate fact
Since Sacha is having trouble posting directly the list I will
forward his latest message since It addresses my second set of
questions:
Begin forwarded message:
From: Alexandre OURJOUMTSEV
Thank you, Richard, for your questions !
Unfortunately, I failed to pass my mail to the CCP4bb - I
s actually over-
determined if one had access to the full molecular transform, so we
are always only using bits and pieces of it in crystallography. But
to what extent that can, in principle, be abused by leaving out low
resolution I would like to know.
Richard Gillilan
MacCHESS
cases?
Richard Gillilan
MacCHESS
There was a detailed and useful discussion of this on this list back
around Dec 1, 2003. If you search in the archives for "I on sig I"
you will find it.
Best
Richard
On Dec 10, 2008, at 5:14 PM, ANDY DODDS wrote:
Hi,
does anyone have a definition of I Sigma I please. Any definitions
t
looking is "coherent diffraction
imaging" ... I think C. Riekel et. al. just published a Phys Rev
Letter on this subject.
Richard Gillilan
MacCHESS
confined spaces, weak magnets are a problem.
Richard Gillilan
MacCHESS
On Jul 21, 2008, at 2:39 PM, Edward Snell wrote:
This reminded me of a haunted beamline that removed crystals from
the loop.
You'd loop the crystals up nicely, block the stream, transfer the
crystal fast to the gonio
nterest. I would love to find some
references to simple estimates based on these parameters. Best I have
seen so far is a paper by Sarvestani et. al. (J. Appl. Cryst. (1998)
31 899-909, but it is a detailed simulation rather than a single
formula.
Richard Gillilan
MacCHESS
water positions.
Thanks
Richard Gillilan
MacCHESS
Several people have asked about the concentrations we use for various
dyes. In the case of fluorescein, we started with 45mg/ml as a stock
solution. This is quite arbitrary and we often found that our initial
stock solutions needed to be diluted 1:10 or 1:100 before use. It is
more art than
s opposed to soaked. Not
sure how significant that effect is. Obviously a dye could
potentially induce conformational or oligomeric changes in some cases.
Richard Gillilan
MacCHESS
Ithaca, NY
On Jun 14, 2008, at 4:51 PM, Mark Del Campo wrote:
Before I place an order for some Izit, are there s
ested users should contact Kathy Dedrick [EMAIL PROTECTED]
Best
Richard Gillilan
MacCHESS, Cornell
Ithaca NY
;s up with Fit2D? Is it still being supported?
Richard Gillilan
MacCHESS
Cornell
schedule for new contributions.
Submit your abstract online at this link: www.amercrystalassn.org/
AbsSubmit/
Microcrystallography Session ACA 2008, Knoxville TN
(Session 13.14, Thursday June 5)
Organizers: Richard Gillilan, Ruslan Sanishvili
Frontiers of structural biology are continuously
Oops, sorry. The x axis of the previous plot is actually not
resolution, but Q. My bad.
Richard
On Nov 27, 2007, at 11:26 AM, Richard Gillilan wrote:
Just a couple small images that may be of interest. The x scale is
resolution in Angstroms, the y scale is intensity (arbitrary
units). I
;s hard to tell on the scale of the plot.
Normally, this kind of small-angle scattering does not show up in PX,
but it is very clear in SAXS when you have a vacuum flight path etc.
Richard Gillilan
MacCHESS
Cornell
the smallest
beamstop. Next time, I'll have to whip out a ruler and see what
distance makes them happy.
It would be interesting to know typical distances for other
facilities. Anyone else made these measurements?
Richard Gillilan
MacCHESS
Note the density of air is approximately 1000
7;s a good
idea. Unfortunately the datasets were kept incomplete on purpose to
reduce possible radiation damage effects.
Richard
On Nov 26, 2007, at 11:38 AM, Juergen Bosch wrote:
Richard Gillilan wrote:
I am currently working on guidelines for when helium and
microbeam are necessary
ally
a factor that regular users have any control over. I don't have any
hard data on this.
Richard Gillilan
MacCHESS
be considered for the Etter Student Lecturer Award
if invited to speak. A limited amount of funds will be available for
speakers from outside the U.S. Please contact Richard Gillilan for
details: [EMAIL PROTECTED]
The deadline for online abstract submission is December 15, 2007
are supported.
Please contact Kathy Dedrick ([EMAIL PROTECTED]) for information on
how to apply for microbeam time at MacCHESS f1 station.
Richard Gillilan
MacCHESS
Cornell University
or engineering with
small crystals, we would love to hear from you. The official link is
www.biochem.utah.edu/aca2007/abstracts.html
Session 13.08. (Gerd Rosenbaum & Richard Gillilan, organizers).
Weds July 25, 2007 morning, (Salt Lake City,
be larger for smaller TLS
groups. This is
just a rule-of-thumb, but would make me suspicious whether the TLS
refinement
was really stable in this case.
Regards
Martyn
-Original Message-
From: CCP4 bulletin board on behalf of Richard Gillilan
Sent: Sun 2/25/2007 1:10 PM
To: CCP4BB@JISC
alues, but it is unclear to me if Refmac5
refinement applies any such constraint.
Can anyone confirm this?
If this is the case, then principle axes of ANISO records generated
from TLSANL are also questionable for these particular bodies as are
thermal ellipsoids.
Richard Gillilan
MacCHES
-0.217 -0.728 0.650
-12.276 102.55 136.73 49.45
MEAN LIBRATION (TRACE/
3)42.390
Anyone seen this happen before?
Richard Gillilan
MacCHESS
anyone is interested, I
would be happy to supply the code and notes, such as they are.
Richard Gillilan
MacCHESS
es of the thermal ellipsoids
for each atom?
Richard Gillilan
MacCHESS
Cornell
density is well resolved
enough to warrant deposition.
How much would you, as a reader, want to see? Crystallization
conditions, unit cell, space group? Omit maps with very partially-
built ligand? Nothing at all?
Richard Gillilan
MacCHESS
Cornell
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