For some ideas on cryocrystallography, one can watch an online webinar on the
subject:
http://www.rigaku.com/protein/webinar-001.html
Maybe some "unbiased" folks can comment? ;)
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Leonard
All the currently used diffraction image processing programs can tell the
crystal orientation from a single diffraction image.
Some programs like d*TREK can calculate new orientations for the crystal if the
crystal is mounted on a reasonable goniometer such as the Rigaku Kappa
goniostat or the
A source of confusion is that we are using two different definitions of
"origin". In the a graphics program sense (coot, pymol), the origin is always
at xyz coordinate (0, 0, 0). I think that's what Napo means by "present the
same cell and origin."
However, imagine a crystal upon which we pu
Any cacodylate buffer will cause gas to be produced. One only needs a minute
exposure on a modern home lab source to see this happening. I suggest that
everyone avoid cacodylate in their crystallization drops that end up being
exposed to X-rays.
Jim
F
If you edit the PDB file "by hand", then you should have no problems. Some
folks might cringe at this, but this does work:
1. Like Roger Rowlett said, "place atom at pointer". You can place a chloride
there. Be sure to add to your molecule and not a new molecule.
2. Save the coordinates to a
Folks may wish to watch a webinar I gave on using HKL3000. In the webinar I
describe how to calculate an Rmeas from scalepack output and also discuss a few
other "how-to" operations.
See www.rigaku.com/protein/webinars-past.html for more viewing pleasure.
Jim
___
When you crystallized your lysozyme, did you have any other anomalous
scattering atoms in the conditions? I am thinking of chloride ions in
particular, but there could be many others. How did you distinguish between
sites of xenon and sites of other kinds of atoms in your analysis?
Did you do
Just a thought for those that mentioned propane and ethane, I would like to
suggest that they try carbon tetrafluoride (CF4) instead. It certainly should
be much safer. It melts at 90 K and boils at 145 K, so you know you are below
145 K if you see it as a liquid.
There could be many causes for this. Perhaps you do not have the best def.site
file for your detector / beamline / hardware. What do your local HKL2000
experts tell you?
You could e-mail me an image and I can help you.
Jim
From: CCP4 bulletin board [C
In addition to reducing the beam divergence, you may wish to use a smaller beam
size by using a smaller collimator or making the slits smaller. A smaller
crystal can also help to spatially separate the Bragg spots as can moving the
detector closer to the crystal. Yes, closer to the crystal. Th
The first Rigaku R-AXIS IIC in North America were installed in late 1990 at
Yale University and McMaster University. That's the same year the Hubble
Telescope went into space and the first search engine Archie was released.
The last R-AXIS IIC shipped in 1994. So these are really vintage syste
I am aware that some programs report interesting numbers.
In addition to what Andrew wrote about resolution cutoffs and "truncated"
reflections, I'd like to mention another issue with systematically absent
reflections.
The number of observations or reflections that come from an integration prog
Rigaku ACTOR robots can accept many different styles of pucks depending on the
LN2 dewar baseplate that the particular ACTOR is equipped with. Rigaku in
China will sell ACTOR pucks, but if you are looking for ALS-style pucks or
ESRF-style pucks or Unipucks or ???, then I am not sure where to ge
Iodide is a fantastic derivative. One does not need a lot with modern X-ray
equipment, careful data collection, and great software.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Rajesh Kumar
[ccp4...@hotmail.com]
Sent: Thursday, May 03, 2012 8:5
Please see my poster at the ACA 2012 meeting. See also:
(1) Dauter, Z., Dauter, M. & Rajashankar, K.R. (2000) Acta Cryst. D56, 232-237.
(2) Nagem, R.A.P, Dauter, Z. & Polikarpov, I. (2001) Acta Cryst. D57, 996-1002.
:)
From: CCP4 bulletin board [CCP4BB@JISCMAIL.A
Here is a trick which I will attribute to Cambridge:
Fill balloon with gas. Put end of balloon over 15 ml Falcon tube. Put Falcon
tube in LN2. No wasted gas.
I would recommend CF4 or carbon tetrafluoride instead of propane though. CF4
is cheap and non-dangerous.
Jim
_
As with all reagents used in the lab it is best to understand the health
hazards. Thanks for note.
Jim
From: Jacob Keller [j-kell...@fsm.northwestern.edu]
Sent: Monday, May 21, 2012 5:22 PM
To: Jim Pflugrath
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb
It may be time for our annual I/sigmaI discussion.
Please note that is what the RCSB expects from you and it is
generally lower than /. Some packages do not output
in an obvious place for you to put in your Table 1. :)
On Wed, 6 Oct 2010, Ed Pozharski wrote:
You don't need twinning to
Zbyszek,
Since you mention I/sigmaI in your PDF, do you mean or
/?
Do you mean I/sigmaI (in whatever rendition you choose) for the averaged
unique reflections or the I/sigmaI for the observations?
Also since one can adjust sigmaI in your scalepack program through the use
of the Error Scale Fac
Are these very strong reflections? Do they appear on more than one image?
Are they an artefact of the detector or the image display program?
It reads like you need to run a lane or two with a positive control of some
kind. Can you grow lysozyme, glucose isomerase, hemoglobin or other
crystals of a protein around the same expected molecular weight and try run
on the gel lanes with about the same amount of crystalline volume as your
puta
In general, if the Rmeas or Rmerge is high in the low resolution shells,
then something is not optimal with the data collection.
Bill Shepard has already mentioned the loop vibrating or moving in the
cryogenic gas flow. Other problems could be the goniometer head was loose,
the magnet was loose,
With Izit or other dyes, you might wish to do a positive control with bona
fide protein crystals and a negative control with bona fide salt crystals.
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Matthew Bratkowski
Sent: Tuesday, November 16, 2010 7:58 PM
To: CC
Crystals of tendamistat were grown from hydrochloric acid and solved by MIR.
I do not recall anything special about the heavy atom soaks, so try
everything in your heavy atom closet.
What have you tried that has not worked?
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On B
You should know that your crystal mosaicity is a physical property of your
crystals and the diffraction experiment. Generally, it is anisotropic
though most programs output a single value. How can that single value
describe what is really happening in your experimental data?
You can do anything
Cool the coverslip on the opposite side of the crystal with a chip of dry
ice. Do not freeze the drop. I learned this from Gary Gilliland. Also I
wonder if you can simply move the whole tray into a cooler temperature?
You can imagine that the thermal expansion coefficient of the glass
cover
If you make the images available, maybe I can take a look and try to use
d*TREK. You will need to be selective about the spots used in indexing.
Most programs can add or delete spots manually.
You may wish to make the X-ray beam smaller and try to expose only a small
volume of one of the crystals.
I will offer my view.
I hate stereo glasses and hate stereo in general.
One should be able to see 3D from the depth-cueing and by keeping the view
in motion. For fitting, I like to flip the view by 90 degrees. I know I am
going to move in displayX and displayY, but never in displayZ. I then
As mentioned there is no I/sigmaI rule. Also you need to specify (and
correctly calculate) and not /.
A review of similar articles in the same journal will show what is typical
for the journal. I think you will find that the cutoff varies.
This information can be used in your response to the r
Glycerol is just another additive to crystallizations and a reasonably good
cryoprotectant. Sometimes it helps to grow crystals, sometimes it has no
effect, and sometimes it interferes with crystal growth. Have I covered all
the possiblities?
One thing is the glycerol often makes a protein more
Collect all your diffraction data in your home lab, solve the phase problem,
fit the map, refine, deposit coordinates in the PDB.
_
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Careina Edgooms
Sent: Friday, March 25, 2011 2:40 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject:
Frances Jurnak published a paper in 1986 on PEG impurities and purification.
As I recall, it turns out that different manufacturers put different
additives in PEGs as preservatives. These are generally anti-oxidants.
PEGs do get oxidized.
I suggest you heat up your new PEG solutions to say 80 d
This link should be helpful to many folks here:
http://blog.revolutionanalytics.com/2011/04/250-years-of-bayes-theorem.html
In general, the Rmerge and Rmeas should get better with a lower symmetry
spacegroup, so that's weird.
Maybe you didn't crystallize what you thought you crystallized. Do people
runs gels anymore on crystals to get an idea of what's in the crystal or do
they do MassSpec?
I think another way to go
Yes, reciprocal lattice coordinates are available for reflections with
d*TREK.
My colleague has also written a "reciprocal lattice viewer" which takes
image pixels and transforms them to a reciprocal lattice. I'm sure others
have similar programs.
But in this modern internet age, I would say enli
I always try sugars for everything. There is a cryocrystallography webinar
at rigaku.com with embedded videos on how to do this. 50% to 100% saturated
sugar (sucrose, glucose, trehalose, sorbitol, et al.) in reservoir buffer is
usually what I try. :)
-Original Message-
From: CCP4 bulleti
I wanted to draw everyone's attention to the Cold Spring Harbor Laboratory
2011 X-ray Methods in Structural Biology course which will take place
October 17 through November 1, 2011.
The official course announcement is here:
http://meetings.cshl.edu/courses/c-crys11.shtml Astute viewers of that lin
Since Frank mentioned cryotongs, I wanted to point to a video of their use
on youtube:
http://www.youtube.com/watch?v=ikiF2qpCRKs
Jim
On Wed, 8 Jun 2011, Frank von Delft wrote:
Hi Zhijie --
With all manipulations on the goniometer, I strongly advise what I learnt
from Elspeth Garman: pra
If you make your images available via ftp, I can take a closer look and come
up with plausible explanations and fixes.
Did you lock down the phi-axis?
_
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of bie
gao
Sent: Wednesday, June 22, 2011 11:23 AM
To: CCP4BB@JISCMA
Instead of an imperfect crystal, this can also occur if one chooses the
wrong Bravais lattice type (or spacegroup) to integrate. For example, if
you choose tetragonal when it is really orthorhombic with a ~ b, or if you
choose orthorhombic and beta is 90.2, then you can see that trying to force
th
I would be very careful about any bond to As. I would imagine such
bonds would be very susceptible to radiolysis with typical radiation used
in the diffraction data collection. Have you performed some
diffraction experiments of various time lengths (or flux) and seen what
happens around this
Please clarify:
Did you process the sets separately from the images?
Or did you process 360 degrees of images all the way to scaled, but
unaveraged results, then average reflections from the 5 different rotation
ranges?
Or something else?
With most processing programs that I am aware of, one ca
OK, same space group, but you didn't indicate what the unit cells were.
They are different, right?
_
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ferrol
shariff
Sent: Sunday, July 10, 2011 3:10 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Same protein, different
For each observation or measurement, HKL, d*TREK, and all other common
programs to my knowledge add up the bits of each relfection from its parts.
They do not add parts of of other reflections (even if symmetry-related)
into a reflection. Reflections for which only part of the Bragg peak is
measur
There is always an anomalous signal to be seen if one measures things well
enough. One does not need to be at the edge in order to detect anomalous
scatterers. For example, most (if not all) of the sulfur SAD phasing is
done well away from the sulfur edge.
I will note that you stated that the f
Many programs such as d*TREK (free download) can predict the actual reflns
that would appear on detector given a particular experiment (crystal,
spacegroup, unit cell, detector, detector position, wavelength, etc).
A quick prediction shows that one will get about 3.9-fold redundancy with
the rotat
PEGs have small amounts of anti-oxidants added to them by the manufacturer.
I think different manufacturers may use different compounds.
And you might imagine that PEGs themselves with their -OH groups go from
alcohol to adelhyde to carboxylate.
-Original Message-
From: CCP4 bulletin boa
g decreases more rapidly with increasing detector-to-sample
> distance than Bragg reflections. For example, Jim Pflugrath, in his
> 1999 paper (Acta Cryst 1999 D55 1718-1725) says "Since the X-ray
> background falls off as the square of the distance, the expectation is
> that a
I do not know the effect myself, but the idea of "vibration fee" has been
tossed around a while. I believe that no vibration reduces the amount of
nucleation that one might get, thus a vibration-free environment is
detrimental when screening for hits. If you already have a method to grow
crystals
Rigaku has a couple of Webinars on cryocrystallography that you may wish to
view:
http://www.rigaku.com/protein/webinars.html
Jim
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Claudia Scotti
Sent: Thursday, February 04, 2010 3:55 AM
To: CCP4BB@JISCMAIL.AC.UK
S
If you look at the structure of glycerol and how it binds to your protein,
what other compounds are similar yet probably won't bind? You essentially
are trying to unoptimize substrate binding which is probably easier than
optimizing substrate binding.
It seems to me that possibilities are anythi
20 g/L is the same as 20 mg/ml, isn't it? That does not seem particularly
high to me.
Why not try 200 g/L?
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jan
Rash
Sent: Friday, March 05, 2010 8:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] crystallization o
The weighted mean is used. Wikipedia
http://en.wikipedia.org/wiki/Weighted_mean has the equation(s).
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Eleanor Dodson
Sent: Thursday, March 18, 2010 4:59 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp
In the instance where we grew crystals is isopropanol, we found they also
grew in PEG6000. The best crystals grew in isopropanol, so we just
harvested the crystals into a similar PEG6000 solution. I would imagine
that you can get the crystals to grow in something beside isopropanol
especially now
One might also check the pH of your crystal and the number of hydrogen bond
donors from the putative sulfate (zero?) or the putative phosphate
(non-zero).
I'm alluding to the structures of the sulfate-binding protein and the
phosphate-binding protein from Quiocho's group.
Jim
_
From: CC
Yeah, but how was I/sdI determined? Most programs allow you to multiply
your sdI by any number you want which in turns means that you can create
any I/sdI that you want.
A multiplicity of 11 does not explain a high Rsym to me.
Jim
On Thu, 22 Apr 2010, Frank von Delft wrote:
Yeah, stop worr
I would test several hypotheses. You have a multitude of salts to choose
from. Test them all.
Let me ask you this: What anions can you test? What's already on your
shelf of chemicals? What did you test already?
Jim
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Beha
I thought some of you would enjoy a little conditional probability
discussion found in the NY Times today, since this is a big part of
crystallography nowadays. I'm always on the lookout for good ways to teach
Bayes's theorem.
http://opinionator.blogs.nytimes.com/2010/04/25/chances-are/
Jim
d*TREK will process compressed images with the following extensions: .gz
.bz2 .Z .pck and .cbf
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian
Tickle
Sent: Thursday, May 06, 2010 6:25 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Processing c
It might be instructive to draw a precession-like diagram of your
reflections in reciprocal space. Remember that reciprocal space dimensions
are generally in reciprocal Angstrom and volumes raise those dimensions to
the third power. Thus (1/12)^3 to (1/15)^3 is not a big volume.
How many reflect
Have you tried to use glycerol or ethylene glycol as the precipitant? What
happens when you go to 50% or higher concentrations?
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Roger
Rowlett
Sent: Wednesday, August 25, 2010 9:19 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject
This cryocrystallography webinar lists some common cryoprotectants:
http://www.rigaku.com/protein/webinar-001.html
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Chris
Weichenberger
Sent: Thursday, September 09, 2010 7:34 PM
To: CCP4BB@JISCMAIL.A
See http://www.rigaku.com/protein/crystallization.html for a set of seven
favorites. Add bovine catalase to the list as well.
Jim
On Thu, 22 Feb 2007, Douglas L. Theobald wrote:
Hi all,
I'd like to pick the collective brain of crystallographers on this list --
what are some of the most eas
Of course, the Rigaku system would be the best.
Jim
On Wed, 28 Feb 2007, Sankar Narayanan Manicka wrote:
Hi,
Our lab is planning to buy an X-ray machine for protein crystallography.
Which system would be best for home source, Oxford diffraction system
Xcalibur Nova or a MSC/Rigaku MicroMax-
Hi Ian,
I am happy to read that your users trust d*TREK so much that they simply
click the buttons and away they go. The indexing program within d*TREK
now outputs the following text:
INFO - The above indexing solution is ONLY a hypothesis.
One must confirm the hypothesis by ex
Ethan, very nice web page. I like the discussion of required signal with
respect to one's diffraction experiment and counting statistics in the
results page.
I will use this in my lecture tomorrow on SAD/MAD phasing.
Do you mind putting Sulfur as one of the radio buttons?
Also, do you mind put
Although the peak height of S atoms can be used as an internal yardstick,
one has to worry about differences in occupancy and possibly hetergeneous
sites (i.e. Ca, Mn and Mg) which can confuse the interpretation of the
results.
On Mon, 16 Apr 2007, Eleanor Dodson wrote:
In cases like this I
d*TREK from Rigaku can process these images.
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Yanming Zhang
Sent: Wednesday, May 16, 2007 2:21 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] .sfrm image files
Hi, All,
I have image files with the format o
d*TREK does this - it's dtorient program works for any goniometer as
well. Or use CrystalClear which came with the detectors at U of Texas.
You probably have both these programs already.
Jim
On Mon, 21 May 2007, Bryan W. Lepore wrote:
are there any free programs which, given a diffraction ima
X-ray Methods in Structural Biology
Cold Spring Harbor Laboratory
October 15th-30th, 2007
http://meetings.cshl.edu/courses/c-crys07.shtml
Deadline for applications: June 15th
This year marks the 20th time this course has been taught at Cold Spring
Harbor Laboratory. It is supported with funds
Rigaku Americas Corporation is pleased to announce the availability of
five (5) awards of $500 each to post-doctoral research fellows to help
with the costs of travel to upcoming summer meetings such as the ACA
meeting in Salt Lake City, Utah (July 21-26), the ECM meeting in
Marrakech, Morocco
I just wanted to re-post this in case you know someone who wants some
travel money. Jim
Rigaku Americas Corporation is pleased to announce the availability of five
(5) awards of $500 each to post-doctoral research fellows to help with the
costs of travel to upcoming summer meetings such as t
What is the mosaicity of the unfrozen crystal?
Jim
-Original Message-
From: Mary Fitzgerald <[EMAIL PROTECTED]>
Date: Mon, 9 Jul 2007 18:05:10
To:CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help with reducing crystal mosaicity
Help please!
I'm looking for some new ideas. I have cr
What about CrystalClear from Rigaku?
-Original Message-
From: Peter Zwart <[EMAIL PROTECTED]>
Date: Thu, 12 Jul 2007 08:55:04
To:CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Program to 'visualize' the reciprocal space ?
> I don't think that there is a program available to do what
:
Really? How?
Jim Pflugrath wrote:
What about CrystalClear from Rigaku?
Is there any advantage to bzip2-ing the individual images rather than
making one bzip2-ed tarball with tar cvfj?
Yes. If you have folks sending you images by sftp or e-mail, then you
don't have ensure a tarball of Giga or Tera bytes works. You can send the
smaller multiple files and restart
It has come to my attention that the wavelength of a Copper Kalpha may
have changed over the years. At least this appears to be true if you look
at the International Tables.
What is the currently approved wavelength in Angstrom of a Copper Kalpha
X-ray produced by a X-ray generator with a cop
Peter wrote:
You can edit these to reflect something that is available on the system - I
suspect that replacing the word "Adobe" with an asterisk might work, however
I haven't tried this myself (and I don't know how to easily query the fonts
that are available on the system - perhaps some X11
It probably goes back to the days of using a single-counter diffractometer
where one didn't have multiple Bragg reflections on an image or film pack.
That is, each reflection was collected by itself. Even in a small molecule
crystal data collection nowadays, it would not hurt to have the crystal
c
Folks, I wanted to call your attention to the following position(s)
available at Rigaku.
Thanks, Jim
Scientist/Programmer
Rigaku, the world's largest analytical X-ray company,
is seeking experienced scientific programmers to join
well-recognized Rigaku scientists such as Jim Pflu
Bong angels are probably ideal already!
Please explain, so that I can teach this to my students. :) Jim
Did you grow Malic Acid crystals?
I see no reason why glycerol cannot be the precipitant. I am aware that
at least one protein is crystallized with ethylene glycol as the
precipitant.
On Wed, 9 Jan 2008, JINJIN ZHANG wrote:
Dear All,
I have got large and nice crystals in a condition that
Is there any way to do a search of crystal orientation matrices with a known
cell to find the best fit to the diffraction pattern? The data were collected
on the Pilatus6M detector so I am limited to mosflm and XDS for processing.
d*TREK will easily process Pilatus6M images.
Both packages alwa
There are many excellent review articles about cryocrystallography and
cryoprotectants. Do labs generally have these articles handy in a methods
folder? Do lab heads help their colleagues by making them read them?
Mineral oil is generally not a good oil to use because it changes volume
too m
Hi everyone,
I received a lot of positive e-mails about my post on cryo
methods. One theme was, "Well, what are the papers I should read?"
I know of one such paper published in Methods. I have made the PDF of it
downloadable from our web site at http://www.rigaku.com/cryo/
Cheers,
Jim
Rigaku Americas Corporation is pleased to announce the availability of
five (5) awards of $500 each to post-doctoral research fellows to help
with the costs of travel to upcoming summer meetings such as the ACA
meeting in Knoxville, TN (May 31 - June 5), the IUCr meeting in Osaka
(August 23-31)
I would use all the data myself and report that the model was built from a
a dataset with 74% completeness in the 2.25 to 2.15 Anngstrom shell. I
would not put the number 2.15 A in the manuscript title nor in the poster
title.
For me the acceptable completeness is 90% in the highest resolutio
That's an easy hypothesis to test. Simply set up your drops with the same
conditions except without protein and see if you get crystals. Please let
us know the results. Thanks!
Jim
On Tue, 29 Apr 2008, Sam Stephenson wrote:
Are calcium citrate crystals a common false positive in trays with
(CST)
From: Jim Pflugrath <[EMAIL PROTECTED]>
Subject: 2008 Rigaku Post-doc Summer Travel Bursary Awards
Rigaku Americas Corporation is pleased to announce the availability of five (5)
awards of $500 each to post-doctoral research fellows to help with the costs of
travel to upcoming
Have you thought about phasing off the sulfurs? This is quite a common
technique nowadays.
Jim
On Tue, 27 May 2008, Joe Smith wrote:
Dear all,
Sorry for an off-topic query.
I have been unable to crystallize a Se-met containing protein (8 Met
in 206 amino acids) in the native crystallization
I would like to point out that flash-cooling in liquid propane has the
added complication that the liquid propane can have a range of temperature
and still be liquid. If you use propane you may not know which
temperature you are actually using. The temperature in the exposed layer
of the prop
Jim,
The fact that liquid propane can exist at a range of temperatures is actually
a MAJOR advantage. While you must ensure that the temperature of the liquid
propane is just above its own freezing point, the very high boiling point of
propane ensures that there is liquid-to-solid contact wit
Folks, sorry for the belated announcement, but I noticed the application
deadline is creeping up on us. Jim
X-ray Methods in Structural Biology
Cold Spring Harbor Laboratory
October 13th-28th, 2008
http://meetings.cshl.edu/courses/c-crys08.shtml
Deadline for applications: June 15th
This year
Whatever dye(s) you use, be sure to run some positive and negative
controls to see how the dye really works.
Jim
On Sat, 14 Jun 2008, Mark Del Campo wrote:
Before I place an order for some Izit, are there some other dyes I can
use to check if I've got a protein crystal?
Thanks,
Mark
I've been in that cold room / hutch. I never heard of it being flushed
with LN2. I think that is just to make the room sound cooler.
Jim
On Thu, 19 Jun 2008, Mischa Machius wrote:
Sadly, I have never seen the room being used. Perhaps one of the 'older'
Martinsrieder on the forum has seen it
How would you tell the difference between a unit cell shift and a wavelength
shift when collecting diffraction data at a synchrotron beamline? Well, all
the cell length would scale by the wavelength, so that would be one hint
that the wavelength changed. If a got longer and c got shorter, then it
There is ALWAYS anomalous scattering. You do not have be at the
absorption edge to get it. The question is just whether your experiment
is good enough to detect it.
So your question of "overlapping" always has the answer Yes, but I would
remove the words "absorption edge" from your question.
A good cover -- judiciously used -- goes a very long way in reducing ice
in dewars whether the dewar is made of foam, glass or stainless steel.
If you keep your dewar covered with a lid that extends on the outside of
the dewar down a few centimeters below the dewar edge, you will have
minimal
Ian, are you saying that one might need to know some crystallographic
theory in order to determine space groups? Or can we simply click a few
buttons in a graphical user interface and be done with it?
Jim
On Mon, 15 Dec 2008, Ian Tickle wrote:
But that only means that the SF contribution f
I wonder if the early use of the shortened "structure amplitude" is
because it was a pain to do any typing, word processing, typesetting, etc
before Gutenberg.
But soon crystallographers will be solving all their structures on their
cell phones and also just text messaging manuscripts to edito
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