ntally, it assumes that the consequences of dose are
linear, so you can weight them by the time they spend in the beam. This
makes sense when the dose contrast is relatively low, but how much a
diffraction pattern from a 1:20 ratio mixture of crystal regions at 9.66
MGy and 0.018 MGy looks li
.1, but I have not tested it thoroughly with other cameras. I would
be interested if you find any bugs!
As for what you're missing, could it perhaps be a reversed phi
direction? That might look like a 180-degree rotation.
Good luck!
-James Holton
MAD Scientist
On 12/28/2014 3:12 PM, Ig
"right" pdb, and the occupancy column
then encodes the by-residue map correlation. This file is more useful for
matching up heavy atom constellations.
It ain't elegant. It ain't fast. But I'm pretty sure it works.
-James Holton
MAD Scientist
On Thu, Sep 11, 2014 at 2:44 AM,
real data. After
all, the only difference between signal and noise is that you find the
signal interesting. Your detector doesn't know the difference. To
separate the two you may find that you need to learn as much about the
noise as you do about the signal, and that is what the conc
The CCP4 FFT program does the 90-degree rotation automatically if you
use "DANO=" as the column assignment. The rotation is because anomalous
difference arise from scattering that is 90 degrees out of phase with
"normal" electrons.
-James Holton
MAD Scientist
O
number seeds and you will have a handle on the RMS
variation in your "measurement" of the charge. The END_RAPID.com script
available here:
http://bl831.als.lbl.gov/END/RAPID/end.rapid/Documentation/documentation.htm
can be useful for doing several parallel occupancy refinements with
unit cell,
despite fitting into only 4 bytes instead of the 13 bytes of text some
seem offended to see below. Would that be better? Or worse?
-James Holton
MAD Scientist
On 7/22/2014 4:01 AM, Bernhard Rupp wrote:
I am just morbidly curious what program(s) deliver/mutilate/divine
these cell co
it might be a refreshing change
to do the opposite of trying to keep your protein from oxidizing all the
time. Perhaps even adding a dash of H2O2. The worst your crystals can
do is not diffract.
-James Holton
MAD Scientist
On 7/1/2014 8:54 AM, Tim Gruene wrote:
Dear Maher,
as far
least not in the given orientation.
I fully realize that the implementation of this is easier said than
done, but perhaps it would be worth the effort?
-James Holton
MAD Scientist
On 6/16/2014 3:04 PM, Pavel Afonine wrote:
Hi James,
a remark: different programs may treat occ=0 differe
them with competitive occupancy refinement.
The bulk solvent is actually a very good example of something for which
we see "no evidence" in our electron density maps, yet we model it in
because 1) we know it must be there, and 2) it makes our R factors
lower. What more could you want
inal depositor. All they need is a citation. Presumably, someone
could re-refine 2hr0 against the "data" that were deposited with it.
Possibly showing how to get an R-factor of 0% out of it. I'd definitely
cite that paper.
-James Holton
MAD Scientist
On 5/14/2014 11:01 AM, N
e.cfg
AgentExtraOptions="-defer 0"
/etc/nxserver/node.conf
AGENT_EXTRA_OPTIONS_X="-defer 0"
If this doesn't work try setting the Link Type to "LAN". This may be slower,
but may also work.
Finally, try using "adxv -nopixmap"
HTH!
-James Hol
c "domain size" as the inverse of the effective
coherence length.
But, the long and short of all this is that as long as your detector pixels
are bigger than the "coherence length" the coherence doesn't really
matter.
Hope that makes sense,
-James Holton
MAD Scientist
alternative hypothesis. It is fairly easy to show that one
model fits better than another, but to show that the difference is
"significant" requires error bars, and that's why we developed the RAPID
procedure:
http://dx.doi.org/10.1073/pnas.1302823110
-James Holton
MAD Scientist
et "enough" XEOL signal. Probably depends on how dark the room is.
-James Holton
MAD Scientist
On 2/15/2014 8:36 AM, Richard Gillilan wrote:
My original question was:
Some years ago, I remember hearing about a microscope that used *visible* light
combined with some propriet
e my ano_sfall.com script to generate the calculated structure
factors (with anomalous) and then feed F+ and F- to MLFSOM. You can
also make calculated anomalous Fs with phenix.fmodel. The only trick
with calculated structure factors is that you will often find your
R/Rfree dropping to ~3%, eve
n get by
shaking the model and/or the data and seeing how the parameter you are
trying to measure "jiggles" in response, whether it be a refined
occupancy of a ligand, or the "scale" of the bulk solvent. This is also
what we did in the first reference above to put error bar
"high Z'" structures. Ahem.
Best advice I can give is to try the "usual" approach, but look very
seriously for NCS as early as you can. Then apply building/phasing
packages like shelx{cde}, phenix.autobuild, or the newly-released Crank2.
-James Holton
MAD Scientis
al-space operator? You can check your answer by loading it
up in coot and seeing if symmetry mates clash with the input coordinates.
Yes, its a lot of work to try all these combinations, but that's the annoying
thing about twinning, it opens up a lot of ambiguities.
Good luck!
-James
o-protection conditions.
HTH
-James Holton
MAD Scientist
On 10/3/2013 5:40 AM, Krithika GOkulnath wrote:
I introduce myself as Dr.Krithika Gokulnath, CAS in crystallography and
Biophysics, UNiversity of Madras. I have been working with a cloned protein and
have been successfully able to crystalli
are
crystallographers out there, but to this day nobody has come up with a
"systematic error" that, when accounted for in refinement, gives you a
small-molecule-style R/Rfree for pretty much anything in the PDB. Not
even lysozyme.
-James Holton
MAD Scientist
On 9/5/2013 9:35 AM,
ot; with
only one electron per unit cell. In this way, you can build up anything
you want, but Bragg's genius was in simplifying all this to a little
rule which tells you how much to turn the crystal to see a given spot.
We sort of take this for granted now that we have automated
diffract
issues in the spindle or the mono, doing a
"wedge" is a way around those sources of error. On modern equipment
most of these problems have been solved, but you should still ask your
beamline scientist what they recommend. Only they know best what sort of
design compromises wer
the monochromator you generally don't worry too much
about the n=2 situation for:
n*lambda = 2*d*sin(theta)
because there just aren't any photons at that wavelength. Hope that
makes sense.
-James Holton
MAD Scientist
On 8/20/2013 7:36 AM, Pietro Roversi wrote:
Dear all,
I a
m or change the construct, but
if it diffracted well, you need to work on your sample prep.
-James Holton
MAD Scientist
On 8/20/2013 1:45 PM, Eugene Osipov wrote:
Wow! Unexpected advices! Thank you very much, for addon and Fab!
Ed, you are right in both cases: about my name and protease. I thin
, MAD gives you significantly better phases than SAD.
It just requires a little more patience to collect it properly.
-James Holton
MAD Scientist
On Tue, Aug 20, 2013 at 2:05 PM, Yafang Chen <mailto:yafangche...@gmail.com>> wrote:
Hi All,
I have three datasets of SeMet-incorpora
No matter what the value printed out for Rmerge in the outer shell is, I
recommend using "-" or "n/a" in your paper. This is because
sum(|I-I0|)/sum(I) actually is equal to "n/a" when sum(I) = 0.
-James Holton
MAD Scientist
On Wed, Aug 14, 2013 at 8:41 AM
oward the bottom. Note that
the "beam center" in the image is actually the point where the x-ray beam
passes through the cryo stream, which can be useful for alignment.
If I take the "relative density" across this image of the stream (assuming
"1" at the center and &
ouple in it and verifying that it actually does last for 2
weeks or more without the temperature rising about that of liquid nitrogen.
-James Holton
MAD Scientist
On 7/17/2013 7:33 AM, Mark J van Raaij wrote:
I heard or read (don't remember where) that repeated warming/cooling cycles ar
That sounds like a unit cell repeat to me. Yes, there is such a
thing as modulated lattices, and also something called "Huang
scattering" where long-range correlations (cracks and other mechanical
effects) can give Bragg spots "tails", but where the "tails" end and the
"unit cell" begins is really just a matter of semantics. The molecules
don't actually care what you think the "unit cell" is.
-James Holton
MAD Scientist
cessarily the "resolution of the structure". This latter quantity,
although emotionally charged, really does need to be more well-defined
by this community and preferably in a way that is historically
"stable". You can't just take data that goes to 5.0A and call it
nal device.
As for Gerard's follow up, I remind him of the immortal wisdom of Jack
Handey:
"Maybe in order to understand mankind, we have to look at the word
itself. Basically, it's made up of two separate words — "mank" and
"ind." What do these words mean? I
aking your R/Rfree worse, then you have reached the
limits of current modelling technology and are basically done with
building and refinement. Might as well deposit what you've got and wait
for some future breakthrough to finally come up with an Fcalc that can
explain your Fobs to wi
around 30 for most diffractometers. The source of this
limitation is actually detector calibration. That hasn't exactly been
published yet, except in the detector literature of course
(http://dx.doi.org/10.1063/1.1488674 section IV.B), but who has time to
read that?
-James Holton
MAD S
is not particularly spectacular for white
lines, so I wouldn't expect much more than ~6 electrons from iron.
-James Holton
MAD Scientist
On 6/2/2013 8:47 AM, Edward A. Berry wrote:
Is Ethan Merritt's anomalous scattering page at:
http://www.bmsc.washington.edu/scatter/
down or moved, o
i.org/10.1107/S0021889804025403
and on the thermal spike you can encounter while mounting/unmounting
with cryovials:
http://dx.doi.org/10.1007/s10969-007-9029-0
-James Holton
MAD Scientist
On 5/22/2013 5:38 AM, Careina Edgooms wrote:
Hi
Does anybody know how long one could store a crystal in li
" by physically adding them
together with fit2d:
http://www.esrf.eu/computing/scientific/FIT2D/
which I think can work with Pilatus-style CBF images. Then you can take
your 5x360 images and make new "datasets" from them and see how XDS or
other integration/scaling packages pe
he first dataset as
the "derivative" and do RIP. You can also try mergeing both wavelengths
together and treat it as SAD data, perhaps doing chronological cuts to
minimize rad dam. This is another reason to interleave wavelengths and
inverse beam rapidly: it allows you to "dial&
ound
to bury it. This is equivalent to "I: 100" in the upper left corner of
the ADXV display (the digital baseline is 40 and the "gain" is 1.8 pixel
levels per photon). On a Rayonix "HE" series in "slow" mode, you can
actually get less than 1 photon of n
bye (1914) Ann. Phys. 348, 49-92 is
perhaps one of the most remarkable in all of science. It is the original
reference for the B factor, the Lorentz factor, and also the paper that
ended determinism.
At least, that is how I understand it. I had to return my English
translation of the Debye paper to t
yes, in 1913, people were still hoping there was another explanation
for these two observations, other than that pesky quantum theory. It
was in 1915 that Debye made the key observation that collapsed
determinism as we knew it. I don't think he was very happy about that.
Neither was
to see if something clicks. Maybe even trying
alternative space groups, just in case you screwed that up too. There
may also soon be "automaitc" runs of BALBES based on the sequence
information of the input file. Eventually, the difference between
different "methods" gets mud
no spots. But, if you sweep through 180 degrees during the exposure you
will at least have a nice, pretty symmetric diffraction pattern to look
at for a moment before the disappointment sets in.
-James Holton
MAD Scientist
On 4/15/2013 3:18 AM, Careina Edgooms wrote:
Dear ccp4
I have been
I agree with Nat. There are good GUIs and bad GUIs, just like there are
good command-line programs and bad command-line programs. Bad programs
are easy to write and good ones are hard. Conservation of "work" I think.
-James Holton
MAD Scientist
On 4/12/2013 10:38 AM, Nat Echols
thin the NX session and then (eventually) click on the "OK" button.
But I'd rather just sleep through all that.
-James Holton
MAD Scientist
On 4/11/2013 9:34 AM, Jim Pflugrath wrote:
I think James gets to 'fight' like in the old game of rogue by
pressing the h, j, k, l k
CCP4 has a GUI?
-James Holton
MAD Scientist
On 4/11/2013 5:17 AM, eugene.krissi...@stfc.ac.uk wrote:
Sorry that this was unclear. We assume that updater is used primarily from
ccp4i, where nothing changed (and why it should be used from command line at
all ?:)). The name was changed because
Woops! Sorry. I was thinking Rpim, which is always lower than Rmerge.
Rmeas is always higher, and more correctly estimates the
infinite-multiplicity Rmerge.
Sorry for the confusion, and thanks for the many reminders I just got
about the definition!
-James Holton
MAD Scientist
On 3/29
quot; every ~20 years so that the same
crappy data keeps looking better and better. That's a slippery slope
I'd rather not be on. I think it is important to remember what it is
we are trying to measure, and to be honest and consistent about what
the error bars really are.
But that's
-angle bin.
Yes, I know we probably all take our local well-maintained and
finely-tuned beamline for granted, but that does not mean we should
stop using the only statistic that tells us something might be wrong
with the machine we used to measure our data. That is definitely
worth the ~20 extra bytes it
ms (30 degrees of phase error at 3
A means that the spatial waves at that resolution are "off" by an
average of ~0.25 A). But, that advantage is really only in the initial
stages of phasing, and it fades as soon as the experimental phases start
holding your refinement back more than
irst SeMet was
ribonuclease H (1rnh) in 1990
http://dx.doi.org/10.1126/science.2169648
If anyone knows of earlier cases, I'd like to hear about it!
-James Holton
MAD Scientist
On 3/13/2013 7:38 AM, Alan Cheung wrote:
Hi all - i'm sure this many will know this : when and what was
g this out to me.
-James Holton
MAD Scientist
On 3/13/2013 1:12 PM, Niu Tou wrote:
Dear colleagues,
We have some diffraction data from small peptide crystals, the shape
of diffraction spots looks normal, and resolution is beyond 2A. The
data were collected with 5 degree rotation per image. L
t really is a problem for them, they
might be interested in "licensing" my lossy-compression algorithm. ;)
-James Holton
MAD Scientist
On 3/11/2013 7:50 AM, Pete Meyer wrote:
I use bzip2 as well. In addition, I generally store md5sums of the
images (before and after compression) be
"proportional" to
that.
Nevertheless, purely on theory, I predict you will much more easily
hit "pitfalls" (or quicksand) by trying to normalize "B" directly
instead of first converting it into something more tangible (like a
volume).
That's all I'm sayi
applying fractional power-law or fractional root functions in reciprocal
space (and I don't even want to think about what that does in real space).
exp(-B1*B2*s^2) = ???
-James Holton
MAD Scientist
On 3/4/2013 11:19 AM, Bosch, Juergen wrote:
Yep, I agree calculate the average B per stru
ucture has an average B factor of 80, then suddenly 78
vs 83 doesn't seem all that different (only a 10% change). Basically, a
difference that would be "significant" in a high-resolution structure is
"washed out" by the overall crystallographic B factor of the
low-res
jamesh/workshop2/decaying.mtz
as the derivative. It is about 18% different from frac0.00.mtz (100%
Se, but badly decayed).
Thanks for all the great ideas!
-James Holton
MAD Scientist
On 1/15/2013 2:06 AM, Santosh Panjikar wrote:
Hi James,
The datasets frac.80.mtz to frac.100.mtz are challenging
use a homolog close enough to
build your way out of the resulting density without any anomalous
information at all.
Perhaps the "fairest" way to do this would be to make a 2-dimensional
score? The "frac" of the dataset you used, plus the BLAST2 E-value of
the model you started with v
. For example, a "score" of 0.78 means that the indicated
procedure could solve the frac0.78.mtz dataset, but not the frac0.79.mtz
dataset.
Based on the reports I have gotten back so far, the "difficulty score"
lineup is:
score method
0.86 xds, xscale, right sites, cr
now the autoindexing picks
an indexing convention at random. I flipped it back at the time, but
when I just now went back to get the I(+)/I(-) I went just one step too
far.
Once again, sorry. It was not my intention to waste anyone's time!
-James Holton
MAD Scientist
On 1/12/2013 2:09 P
/~jamesh/challenge/impossible.mtz
md5 sums:
c4bdb32a08c884884229e8080228d166 impossible.mtz
caf05437132841b595be1c0dc1151123 possible.mtz
-James Holton
MAD Scientist
On 1/12/2013 8:25 AM, James Holton wrote:
Fair enough!
I have just now added DANO and I(+)/I(-) to the files. I'll be
corporation ahead of time from
something like mass spec (especially if you knew it could make-or-break
your structure determination). However, I don't think it is "realistic"
that you would know where they are before running shelx.
-James Holton
MAD Scientist
On 1/12/2013 7:46 AM,
ht be able to
use that insight to improve the software, and that is something that
will benefit all of us.
Or, it is entirely possible that I'm just not running the current
software properly! If so, I'd love it if someone who knows better (such
as their developers) could enligh
.92. And yet, one can be solved
automatically, and the other can't.
More details can be found on the web page:
http://bl831.als.lbl.gov/~jamesh/challenge/
But, my question for the CCP4BB is:
Are there any "John Henry"s left out there who can still "beat the
machine"? Anyone?
-James Holton
MAD Scientist
all the other R values
to this resolution as well, since including a lot of zeroes does nothing
but artificially drive up estimates of relative error. Perhaps we
should even take a lesson from our "small molecule" friends and start
reporting "R1", where the R factor is comp
nts go these are all desirable properties. You can get it
from spi.com.
-James Holton
MAD Scientist
On 12/4/2012 6:42 AM, Jens Kaiser wrote:
Ulrike,
I usually suggest it as the second try (the first try is mother liquor
alone), as it does not involve mixing any new buffer concoctions. I
ealing omit" procedure? That's a good
question. However, I am reasonably confident that this "critical
occupancy" is less than 1.0 And probably greater than zero as well.
-James Holton
MAD Scientist
On 11/20/2012 10:36 AM, GRANT MILLS wrote:
Hello all,
I'm curre
incidence, but it does mean that there is
a continuum of states between a sharp "ice ring" and an amorphous "water
ring". Your best diffraction may well be somewhere in the middle.
-James Holton
MAD Scientist
On 11/15/2012 10:12 AM, A Leslie wrote:
Dear Sebastiano,
ocal" correlations in reciprocal space. This is why solvent
flattening works, but it also produces some "bias" in the Rfree. How
much bias? It's actually hard to say. I know of a few people who have
written programs for picking free-R flags in an "unbiased" way,
ar to stably return to the "same" value, or
at least values different enough to say it is Zn vs Ca, then the
identity of your metal sites is NOT well-determined by your data.
-James Holton
MAD Scientist
On 10/30/2012 7:55 PM, Kumar, Veerendra wrote:
Dear CCP4bb users,
I am working on
;SOLVENT NO"
when you do this.
http://www.ysbl.york.ac.uk/refmac/docs/keywords/xray-principal.html#solv
You can actually add multiple partial structures and scale them
independently, but in my hands things start to get crazy if you have
more than 2.
-James Holton
MAD Scientist
On Wed, Sep 26,
s the green line. Very much like what Tim suggested.
Not exactly a problem for typical macromolecular refinement, but
still... I wonder what would happen if I edited my ${CLIBD}/atomsf.lib ?
-James Holton
MAD Scientist
On 9/18/2012 6:32 AM, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE---
e rest of the molecule with "kick maps" to see how
stable the occupancy is. Since refinement only does forward-FFTs, it is
formally insensitive to series termination errors. It is only map
calculation where series termination can become a problem.
Thanks to Garib for clearing up that
ginal Word document. The
latter is somewhat easier to automate.
Sorry!
-James Holton
MAD Scientist
On 9/1/2012 3:48 AM, Rex Palmer wrote:
Dear CCP4BB
Does anyone know how to convert a .pdf file into a meaningful Word file.
Any suggestions will be greatly appreciated. The pdf file has numerou
do is bubble air or N2 through a big vat
of your "reservoir solution" and then direct that bubbled-off gas
through a pipe at your drop. I imagine this would be a great way to
deal with alcohol-based conditions as well (provided you had adequate
ventilation).
-James Holton
MAD Scien
ot;theta"
is the Bragg angle.
For the above PDB, I get:
d sum(F^2)
3.907 121
3.673 156
3.449 111
2.676 88.5
2.255 111
2.075 153
1.953 62.9
1.922 84.2
1.888 62.5
1.836 4.33
1.725 47.8
1.662 1.84
1.527 96.7
1.477 42.8
1.448 39.5
1.375 78.9
1.370 34.6
HTH,
-James Holton
MAD Scientist
On Tue, J
Because sometimes it is important to know how much the structure moved
relative to the unit cell, such as before and after a round of
refinement.
-James Holton
MAD Scientist
On Tue, Jun 19, 2012 at 3:34 PM, Petr Leiman wrote:
> Would anyone be kind enough to explain what kind of informat
)= 1.23212 for N PRO79
MAXD(Bfac)= 1.69for CA GLY 102
Doesn't need a special version of awk, but you may have to edit the top
line to reflect where "awk" is on your computer. Sometimes its in
/bin/awk, or /usr/bin/awk, or (for some reason) /usr/share/awk
-J
rested in reproducing this problem, I have an example
input file and script here:
http://bl831.als.lbl.gov/~jamesh/pickup/for_kevin.tgz
To generate this input file, I used scalepack2mtz, TRUNCATE, and then
MLPHARE. The "test.com" script runs DM. And yes, it did take me a
while to figu
hing ANOMALOUS ON does affect the statistics and the
outlier rejection" in the SCALA manual and decide that they had better
turn off all those evil "anomalous" things. Then they tell their
students to do the same, etc.
-James Holton
MAD Scientist
On Tue, Jun 12, 2012 at 3:17 AM, E
amp;
Thorne (2009) presented a potentially general way of holding a protein
crystal at any temperature you want between 100 and 300K:
http://dx.doi.org/10.1107/S0021889809023553
-James Holton
MAD Scientist
On 5/8/2012 7:16 AM, R. M. Garavito wrote:
Dear Anna,
I know that you already have got
rystals you need if you type in
their size in all three dimensions. but this estimate assumes that you
don't have high concentrations of heavy metals in your solution! So, if
it says you can get away with one crystal but you know your have a
dose-doubling concentration of something, then y
g for your coordinates, then perhaps
there is something wrong with your figures? In a way, this is like
asking an author for a comma-separated list of their raw data points so
that you can re-plot them in Excel. The paper really ought to stand on
its own, clearly showing the evidence needed t
SeMet can be converted
back to SeMet with DTT, but the double-oxidized form cannot.
-James Holton
MAD Scientist
On 4/17/2012 4:03 AM, Uday Kumar wrote:
Hi sarah
I believe, you might have used reducing agent in your SeMet-labeled protein
sample.
if avoiding reducing agent is not a problem to
lso still have certain programs "running out of virtual
memory" at 4GB as well. Despite the fact that the relevant machine has
48 GB of RAM and 80 GB of swap.
I tell you. Technology just doesn't work.
-James Holton
MAD Scientist
On 4/4/2012 2:21 AM, Takanori Nakane wrote:
t; in the fo-fc map. They will also be the last things to poke their
heads above the 1-sigma contour in a 2fo-fc map, but that does not mean
they are "not there". You can lower the map contour and see them easily
enough (even in 3bcl). The trick is having some kind of
statistica
On 4/2/2012 6:03 AM, herman.schreu...@sanofi.com wrote:
If James Holton had been involved, the fabrication would not have been
discovered.
Herman
Uhh. Thanks. I think?
Apologies for remaining uncharacteristically quiet. I have been keeping
up with the discussion, but not sure how much
quot;p-value" would also help solve the problem of the careless and/or
uneducated over-interpreting PDB files. Which is the "right one"? Good
question! I think its time we started dispelling the myth of the
single-conformer protein anyway.
-James Holton
MAD Scientist
O
t; before you can
take advantage of photoelectron escape.
So, for any "regular" native data collection, I'd say: no, wavelength
doesn't matter.
-James Holton
MAD Scientist
On 2/15/2012 3:55 PM, Bart Hazes wrote:
Diffracted intensity goes up by the cube of the wavelength, but so
you have a reviewer complaining that your Rmerge in the
outermost bin is too high, simply tell the editor that you did not use a
3-sigma cutoff on the raw data for the Rmerge calculation, and ask if
he/she would prefer that you did.
-James Holton
MAD Scientist
On 1/27/2012 9:55 AM, Jacob Keller
me before the crystal is dead. So, to
me, "strategy" is nothing more than deciding how to divide up those
shutter-open seconds, and the only way to increase
redundancy/multiplicity is to shorten the exposure time. Which, by the
way, is almost always a good idea.
-James Holton
MAD S
ed a tremendous amount
of time and effort learning it if they are so desperate for you to join
their ranks.
Oh, and don't fall for the "so other people can read your code" trick.
Trust me, NOBODY wants to read your code! Unless, of course, they are
trying to re-write it in the
r you have solved the structure because it
dramatically changes the intensity you have available for any given hkl
index.
-James Holton
MAD Scientist
On 1/19/2012 8:20 AM, arka chakraborty wrote:
Hi all,
Thanks for providing multiple solutions to my problem. Prof . Tim
Gruene and Prof. Ja
at even lemmings have some sense in their tiny
little heads? Do we? Does anyone have a scientifically compelling
reason to call MAD something other than "multiwavelength anomalous
diffraction"?
-James Holton
MAD Scientist
On Wed, Jan 18, 2012 at 12:28 PM, Ethan Merritt
wrote:
ttempts MSAD (mult-SAD), which I think helps differentiate them from
actual MAD data collections where you at least try not to fry the
crystal between measurements that you need to subtract to get your
phasing signal. Unless, of course, you are doing RIP!
Just my humble opinion,
-James
m afraid I don't really have a nice "canned" procedure for making
phase-colored images yet because it is hard to figure out which
intensity scale is most interesting. I suppose I could put the
complex_divide procedure inside of nearBragg, but that would make it run
at least 2x slower,
PHIC ) you will NOT get the bulk solvent
contribution alone. AFAIK there is no way to obtain just the bulk
solvent contribution from REFMAC.
-James Holton
MAD Scientist
On 12/13/2011 6:24 AM, Ed Pozharski wrote:
On Tue, 2011-12-13 at 02:31 +, Yuri Pompeu wrote:
Hi Ed,
I just had a chance of
Since "striking distance" is about 3 microns for the primary
photoelectron and the largest unit cell in the PDB is ~0.1 microns long,
I think that means all bets are off when trying to "connect" energy
absorbed by a heavy atom to damage somewhere else in the unit cell.
Sounds like rad dam to me. See Burmeister, W. (2000)."Structural
changes in a cryo-cooled protein crystal owing to radiation damage",
Acta Cryst. D 56, 328-341. The first sign of a Met loosing its S-CH3
group will be a negative difference peak on the S.
-James Holton
MAD Scient
ression"
implies a dose-rate effect, the converse is not necessarily true. There
is much debate about this in the rad dam field, but it seems whenever a
traditionally-held belief like "dark progression" is challenged, the
rest of the MX community seems to dismiss it as "oh, you&#x
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