/END/RAPID/end.rapid/Documentation/documentation.htm
can be useful for doing several parallel occupancy refinements with the
benefit of also adding noise to the data to get a more realistic error bar.
HTH
-James Holton
MAD Scientist
On 8/28/2014 7:49 AM, Alejandro Virrueta wrote:
Hello,
I am
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
On 8/29/2014 11:43 AM, Alexander
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 constants in recent
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 as I understand, the anomalous scattering comes from inner shell
electrons
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 differently. In
phenix.refine (phenix.maps, etc) atoms with zero occupancy
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?
-James Holton
MAD Scientist
On 6/13/2014 7:45 PM, Frank von Delft
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 Holton
MAD Scientist
On 5/3/2014 2:34 PM, Cedric Govaerts
coherence in this way. Some might
even define the mosaic 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
of waters model is
always an 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
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 proprietary image processing algorithm
with phenix.fmodel. The only trick
with calculated structure factors is that you will often find your
R/Rfree dropping to ~3%, even when every conceivable source of
experimental noise has been included. That's a problem I'm still
working on.
-James Holton
MAD Scientist
On 2/13/2014 6:54 AM, Mooers
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 bars on the
electron density itself.
-James Holton
MAD Scientist
On Wed, Feb 5, 2014
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 Scientist
On 1/18/2014 11:18 PM, Felix Frolow wrote:
Francis, It can happened
We have (not yet published) P1
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 Holton
MAD Scientist
On 12/14/2013 6:44 AM, D Bonsor wrote:
Dear all,
I have collected ~160
spots at low angle, and the d-spacing of the
innermost spots is at least big enough to fit your protein inside it in
P1 with a bit of solvent left over.
If you do have ice, then it is still possible you had a protein crystal,
and just need to work on cryo-protection conditions.
HTH
-James
much anything in the PDB. Not
even lysozyme.
-James Holton
MAD Scientist
On 9/5/2013 9:35 AM, Alastair Fyfe wrote:
Below are some links to tools for simulating Fobs data:
phenix.fake_f_obs:
http://cci.lbl.gov/cctbx_sources/mmtbx/command_line/fake_f_obs.py
phenix.fmodel:
http://cci.lbl.gov
.
-James Holton
MAD Scientist
On 8/22/2013 12:57 AM, herman.schreu...@sanofi.com wrote:
Dear James,
thank you very much for this answer. I had also been wondering about it. To
clearify it for myself, and maybe for a few other bulletin board readers, I
reworked the Bragg formula to:
sin(theta
you get for one machine may or may not apply to
the next one you use!
-James Holton
BADAS Scientist
On 8/22/2013 4:10 AM, Alexander Batyuk wrote:
Dear James,
Could you elaborate on the inverse beam protocol a little more in details,
especially, on round robin, please? What would be the ideal
.
-James Holton
MAD Scientist
On Tue, Aug 20, 2013 at 2:05 PM, Yafang Chen yafangche...@gmail.com
mailto:yafangche...@gmail.com wrote:
Hi All,
I have three datasets of SeMet-incorporated protein at peak, infl
and high wavelength respectively. SAD with peak dataset works well
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, Pietro Roversi
pietro.rove
and 0 beyond the edges), I get an average of 60%, which
brings 5611 ADU/pixel down to 3366 ADU/pixel, vs the observed 3600
ADU/pixel. Not too bad, I think.
-James Holton
MAD Scientist
On Thu, Aug 1, 2013 at 9:31 AM, Pietro Roversi
pietro.rove...@bioch.ox.ac.uk wrote:
Dear all,
together
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 are what can
make the dewars less efficient and can break them.
So we keep them always
a matter of semantics. The molecules
don't actually care what you think the unit cell is.
-James Holton
MAD Scientist
the intensities drop into the noise at 5A, but that is never
going to be as good as using data that does not drop into the noise
until 4.5A.
-James Holton
MAD Scientist
On 6/27/2013 9:30 AM, Ian Tickle wrote:
On 22 June 2013 19:39, Douglas Theobald dtheob...@brandeis.edu
mailto:dtheob
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? It's a mystery, and that's why so is
mankind.
-James Holton
MAD
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 within sigma(Fobs).
-James Holton
MAD Scientist
On 6/26/2013 12:08 AM, herman.schreu...@sanofi.com
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, or the firewall I'm behind is blocking it?
I want
. 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 Scientist
On 6/2/2013 12:43 PM, Edward A. Berry
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 liquid
nitrogen for before it will no longer diffract
synchrotron trip to try out new data collection strategies on YOUR
crystals. Particularly the attenuate and expose longer (attenu-wait)
strategy. If you get the same or better data quality going fast as you
do going slow, then great! Keep doing it. At least, until the next
upgrade.
-James Holton
MAD
. This is another reason to interleave wavelengths and
inverse beam rapidly: it allows you to dial the rad dam by using the
image file time stamps. So, in this way, this strategy let's you try
three methods for the price of one.
-James Holton
MAD Scientist
On 5/16/2013 10:03 AM, Gerard Bricogne wrote
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 perform when the same photons are
divided over more or fewer images.
-James Holton
MAD Scientist
On 5/16/2013 10:25 AM, Frank von Delft wrote
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 Einstein.
-James Holton
MAD Scientist
. 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 the library. I'll order my own copy.
-James Holton
MAD Scientist
On Fri, Apr 19, 2013 at 2
. 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 performing
, the difference between
different methods gets muddied. Then your average depositor will be
even more unsure about what to put into REMARK 200, and people like me
will be endlessly asking for command-line options that turn these
features off.
-James Holton
MAD Scientist
On 4/15/2013 6:48 AM, Raji
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 keys on his keyboard (not a detachable one
either). While Eugene gets
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 wrote
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
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 takes up in your paper.
-James Holton
MAD Scientist
On Fri, Mar 29
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 just my opinion. I could be wrong.
-James Holton
MAD Scientist
On Fri
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
) 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 the
first protein structure solved on a synchrotron
holding your refinement back more than they help (which actually happens
rather quickly). Remember, the 'bulk solvent' model, as far as the
phases are concerned, is really just another kind of solvent flattening.
-James Holton
MAD Scientist
On 3/14/2013 5:27 PM, Guangyu Zhu wrote:
I have
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. Later on we
-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) because it's quicker to check
the hash for validity than load up the images - but this may be overkill
.
Whether or not a 10% difference is significant depends on how accurate
you think your B factors are. If you kick your coordinates (aka using
noise in PDBSET) and re-refine, how much do the final B factors change?
-James Holton
MAD Scientist
On 2/25/2013 12:08 PM, Yarrow Madrona wrote:
Hello
to
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 structure
directly
instead of first converting it into something more tangible (like a
volume).
That's all I'm sayin'
-James Holton
MAD Scientist
On Mon, Mar 4, 2013 at 12:31 PM, John Fisher johncfishe...@gmail.com wrote:
Seriously?
I believe this specific forum has become quicksand rather than a useful
% 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 to solve using SAD
phasing. However these datasets can
so far, the difficulty score
lineup is:
score method
0.86 xds, xscale, right sites, crank2 (Pavol Skubak)
0.78 xds, xscale, right sites, mlphare, dm, phenix.autobuild using 20
models (James Holton)
0.75 xds, xscale, right sites, mlphare, dm, buccaneer/refmac/dm (James
Holton)
0.71
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 vs the 3dko sequence?
-James Holton
MAD Scientist
On Mon, Jan 14, 2013 at 2:31 PM, Nat
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 enlighten me.
-James Holton
MAD Scientist
On 1/12/2013 3:07 AM, Pavol Skubak wrote:
Dear James,
your challenge in its current form ignores an important
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, George Sheldrick wrote:
Dear James,
I
/~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 very
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 PM, George Sheldrick wrote
.
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 Henrys left out there who can still beat the
machine? Anyone?
-James Holton
MAD Scientist
, 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 computed only for hkls where
I/sigma(I) is above 3?
-James Holton
MAD
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 do
not have hard data, but I'd
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 currently working on a structure which if I stub a certain side
chain phenix/coot shows me a large green blob which looks
away from NCS, unless I'm really sure that
there is nothing funny going on in the crystal symmetry.
-James Holton
MAD Scientist
On 11/13/2012 1:55 AM, vincent Chaptal wrote:
Dear all,
I am not sure I understand point groups and relations between groups
and subgroups anymore, and would
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,
This is not entirely straight-forward.
The Oxford English dictionary gives the first definition
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 a Ca2+ binding protein. it has 4-5 ca2+ binding sites. I
purified the protein in presence
://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, 2012 at 11:45 AM, Kiran Kulkarni
dr.kirankulka
.
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-
Hash: SHA1
Hello Oliver,
when you fit
!
-James Holton
MAD Scientist
On 9/15/2012 3:12 AM, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Ian,
provided that f(s) is given by the formula in the Cromer/Mann article,
which I believe we have agreed on, the inset of Fig.1 of the Science
article we are talking about
.
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 numerous
figures and tables.
Rex Palmer
http://www.bbk.ac.uk/biology/our
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 Scientist
On 7/10/2012 9:28 AM, m zhang wrote:
regaentDear All,
I am sure this question was discussed
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, Jun 26, 2012 at 2:34 PM, Edward A. Berry ber...@upstate.edu wrote:
Maybe figure 4 in
Viatcheslav Berejnov et al. Vitrification of aqueous solutions
J. Appl
)= 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
-James Holton
MAD
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 petr.lei...@epfl.ch wrote:
Would anyone be kind enough to explain what kind
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 figure this out.
-James Holton
MAD Scientist
On 6/14/2012 4:58 AM, Appu kumar wrote
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 you're going to need to
average data from two crystals, etc.
Good luck!
-James Holton
MAD Scientist
On 5/3/2012 8:29 AM, Jacob Keller
points so
that you can re-plot them in Excel. The paper really ought to stand on
its own, clearly showing the evidence needed to support the conclusions
drawn. Or at least that is what I was taught in scientist school.
-James Holton
MAD Scientist
On 4/18/2012 3:34 PM, Marc Kvansakul wrote
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 your
of
statistically-sound rule for being sure. Otherwise, we might start
seeing map contour creep, just as we currently see R factor creep in
high-profile journals.
-James Holton
MAD Scientist
On 4/10/2012 1:04 PM, Francis E Reyes wrote:
Dale
Thank you for the case study. I will certainly
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:
Dear Tim,
64-bit is about memory addressing - why would you expect a performance
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
of the
single-conformer protein anyway.
-James Holton
MAD Scientist
On 3/26/2012 7:40 AM, Ed Pozharski wrote:
On Mon, 2012-03-26 at 10:17 -0400, Gregory Bowman wrote:
But what about the issue of resolution? As was previously pointed out,
at say 3.2 Å resolution, many side chains will fail
: 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
does absorption and I don't know exactly about radiation damage. One
interesting point is that on image plate and CCD detectors
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 Scientist
On 1/24/2012 11:52 AM, Miguel Ortiz Lombardia wrote:
El 24/01/12 18:56, Greg
read your code trick.
Trust me, NOBODY wants to read your code! Unless, of course, they are
trying to re-write it in their favorite language.
-James Holton
MAD Scientist
On 1/23/2012 8:46 PM, Yuri Pompeu wrote:
Hello Everyone,
I want to play around with some coding/programming. Just simple
anomalous
diffraction?
-James Holton
MAD Scientist
On Wed, Jan 18, 2012 at 12:28 PM, Ethan Merritt
merr...@u.washington.edu wrote:
On Wednesday, 18 January 2012, Soisson, Stephen M wrote:
But if we were to follow that convention we would have been stuck with
Multi-wavelength Resonant
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. James Holton
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 Holton
MAD Scientist
On 1/18/2012 3:08 AM, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash
of nearBragg, but that would make it run
at least 2x slower, and it is already slow enough!
-James Holton
MAD Scientist
On 1/9/2012 11:13 PM, 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
actually
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 looking
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 Scientist
On 11/22
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.
-James Holton
MAD Scientist
progression is challenged, the
rest of the MX community seems to dismiss it as oh, you're just working
on lysozyme. Well, what should we be working on?
-James Holton
MAD Scientist
On 11/20/2011 5:22 PM, Sanishvili, Ruslan wrote:
Hi James,
I don't think the comment you referenced meant
an idea of the expected rate of decay,
then wait for a while and start shooting again. Do you see
significantly worse diffraction?
-James Holton
MAD Scientist
On 11/18/2011 1:50 AM, Mark J van Raaij wrote:
I.e. if you collect one image and then wait until the orientation and
strategy
the scaling
B-factor, which will change about 1 B-factor unit per MGy (Kmetko et
al. 2006).
-James Holton
MAD Scientist
On 11/17/2011 6:36 AM, Jacob Keller wrote:
I also have seen similar. I was thinking it was potentially some kind
of radiation damage? Is there a good paper which examines what
of datasets to deal
with down to less than 10. Perhaps even less than 1.
-James Holton
MAD Scientist
On 11/8/2011 5:17 AM, Graeme Winter wrote:
Dear Herbert,
Sorry, the point I was getting at was that the process is one way, but
if it is also *destructive* i.e. the original master
? Or is it just too repugnant to have
modified the data in any way shape or form ... after the detector
manufacturer's software has corrected it? Would it suffice to simply
supply a couple of example images for download instead?
-James Holton
MAD Scientist
be wasting my
time developing this further? Will the crystallographic world simply
turn up its collective nose at lossy images? Even if it means waiting
6 years for Nielsen's Law to make up the difference in network
bandwidth?
-James Holton
MAD Scientist
On Mon, Nov 7, 2011 at 10:01 AM, Herbert J
to the
width of the relevant Ee_ff(x,0) function.
Ian has also pointed out that none of this considers the mechanics of
how you actually calculate maps, where things like series termination
error come into play. But perhaps that is a topic for a new thread?
-James Holton
MAD Scientist
On 11/2
aggressive outlier rejection in
scaling. Can't remember if that ever got published...
-James Holton
MAD Scientist
On 11/2/2011 1:33 AM, Graeme Winter wrote:
Hi Ed,
Ok, I'll bite: I would be very interested to see any data sets which
initially were thought to be e.g. PG222 and scale OK ish
factor are blurred out by the much wider
B-factor Gaussian. It doesn't hurt to model the atoms form factors
properly, but in almost all cases of MX, some other source of error is
more important.
-James Holton
MAD Scientist
On 11/1/2011 6:55 AM, Ed Pozharski wrote:
On Mon, 2011-10-31 at 15
images is higher, but I
think the potential benefits to the structural biology community if we
can crack the 0.1% S-SAD barrier is nothing short of revolutionary.
-James Holton
MAD Scientist
On 11/1/2011 8:32 AM, Anastassis Perrakis wrote:
Dear Gerard
Isolating your main points
version of
${CLIBD}/atomsf.lib at:
http://bl831.als.lbl.gov/~jamesh/pickup/all_atomff.gnuplot
in gnuplot you can type:
load 'all_atomff.gnuplot'
plot Mg_plus_2_ff(x,20), O_ff(x,15)+2*H_ff(x,15)
and stuff like that.
-James Holton
MAD Scientist
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