rier terms in
the map. By that metric I believe rubisco is still the champion of
"information content" in the PDB.
-James Holton
MAD Scientist
On 6/9/2020 6:54 AM, Edward Snell wrote:
I’m reminded of a comment Wim Hol made at an ACA meeting many years
ago during a discussion of resoluti
not be there. Titratable ones for example. The
philisophy explained to me once by Garib is that since it is twice as
bad to put in an electron that isn't there vs leaving out one that is
you want to err on the side of dropping hydrogens that don't seem to fit.
HTH,
-James Holton
MAD Sc
you?
-James Holton
MAD Scientist
On 5/27/2020 6:49 PM, Jessica Bruhn wrote:
Hello,
I am wondering if pseudosymmetry can cause weak reflections that mimic
the doubling of one unit cell axis' length. Has anyone seen something
like this before?
I am processing data from a small molecule sample
runs sfall with the right axis
order in the event it comes up:
http://bl831.als.lbl.gov/~jamesh/pickup/ano_sfall.com
-James Holton
MAD Scientist
On 5/14/2020 3:28 PM, Bernhard Rupp wrote:
Thanks to all. Mapmask works. Yes the order to change to is ZXY. Map
from coefficients indeed
; in sfall. There are still some "gotcha" space groups in the SFALL
code for density near cell edges. I can't remember which ones now
because years ago I started using SFSG 1 and the problem went away.
-James Holton
MAD Scientist
On 5/14/2020 1:44 PM, Bernhard Rupp wrote:
Hi Fellows,
I am f
,
not before.
On 5/7/2020 9:06 AM, James Holton wrote:
Ah! I did that last formula wrong. Never do algebra in your head
without checking. It should be:
The equation then becomes:
f = P/t/L/1.2e-5
Where 1.2e-5 = 0.2 cm^2/g * 1.2 g/cm^3 * 1e-4 cm/micron * 50%, f=flux
and t=exposure
rule, it is
here:
https://doi.org/10.1107/S0909049509004361
And, of course, if you are lucky enough to have accurate flux, size and
shape information for the beam and sample, plus chemical composition the
most accurate dose you'll get from raddose-3D: https://www.raddo.se/
-James Holton
MAD
in). A few considerations, yes, but
it can be a good sanity check.
-James Holton
MAD Scientist
On 5/5/2020 11:48 AM, Murpholino Peligro wrote:
Do diffraction patterns publicly accessible contain information about
the x-ray
is quite a
bit less than tha main illumination. This is true for all kinds of light.
-James Holton
MAD Scientist
On 5/5/2020 11:59 PM, Tim Gruene wrote:
Hi James,
for us, the suggestions of cling film / plastic wrap or just swapping
keyboards and mice per person is the simplest - thanks
bly bleach and flake with prolonged exposure. Ever seen a
keyboard left out in the sun for a few weeks? I'd worry a bit about
this micro-damage creating crevices where bugs could hide.
I encourage you to bring this up with your Health and Safety people, but
make sure they are sitting down first
Because as soon as I put on gloves my nose starts to itch.
On 4/29/2020 12:37 PM, gianluca.sant...@esrf.fr wrote:
ISO keyboards are bad.
But why not just using disposable gloves to operate the instruments?
On April 29, 2020 9:30:19 PM GMT+02:00, James Holton
wrote:
Keyboards are cheap
accurate than Iobs, which is the typical result of
small-molecule refinements. I expect that is why they are not nearly as
afraid of twinning as we are.
-James Holton
MAD Scientist
On 4/28/2020 2:19 PM, Frank von Delft wrote:
Hi all - feel free to point me to the docs if it's already clear
som
Keyboards are cheap. Why not everyone get their own?
Then we can all stop fighting about whether the key should be
shaped like an "L" or not.
-James Holton
MAD Scientist
On 4/29/2020 11:53 AM, Tim Gruene wrote:
Dear all,
can you make suggestions for how to disinfect computer
with individual pixels only a few
nanoseconds apart. It should be possible to differentiate the light
from a long-lived fluorophore from background. However, I don't think
anyone has tried that yet.
-James Holton
MAD Scientist
On 4/4/2020 5:48 PM, Jurgen Bosch wrote:
Here’s another link I
or pine genomes? I
doubt it, but I also doubt that anyone has checked.
Thank you for the suggestions so far! Very interesting and helpful!
-James Holton
MAD Scientist
On 3/31/2020 11:46 PM, Sahil Batra wrote:
Dear Prof. Holton,
An innovative idea; however all of the 30 kb genome may not
NMR spectroscopists are ~50 years ahead of us on this. They call it
"zero filling". Fortunately, these extra data compress very well.
-James Holton
MAD Scientist
On 3/31/2020 9:36 PM, Petr Kolenko wrote:
Dear colleagues,
We, the developers of a program for paired refinement,
s in already in the hand of half the people on
the planet.
Comments? Insights?
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
thy. None of us are easily
replaced, and there is a lot of work to do.
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
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wouldn't want
to try crystallizing the whole thing, but I wonder if this might be an
excellent target for cryoEM? A challenge for that "we can classify our
way out of anything" philosophy? And the result would most certainly be
interesting.
-James Holton
MAD Scientist
On 3/21/20
paper says it is a transcription factor that up-regulates
chaperones, another says it is a secreted imunosuppressor.
So, my question remains: why haven't we solved it yet?
-James Holton
MAD Scientist
On 3/21/2020 9:12 AM, Rigden, Dan wrote:
Hi James
5o32I is not a homolog of ORF8 - the BLAST e
ologous region contains the S84L site
(Val I544 in 5o32). I had a quick look and appears to be a
cavity-filling mutation to me. Not very big, but maybe something could
fit in there. To be sure we'd need a structure of ORF8.
Good luck to you all, and stay healthy.
-James Holton
MAD Scientist
reen peak in one part of the map without creating red peaks elsewhere.
You only have 2-3 numbers to play with and they impact every nook and
cranny in your model. If bulk can't be made to explain the difference
peak, then try modelling a water into that peak, and then look at the
bulk solvent
I'd say they are 1 bit each, since they are the answer to a yes-or-no
question.
-James Holton
MAD Scientist
On 2/27/2020 6:32 PM, Keller, Jacob wrote:
How would one evaluate the information content of systematic absences?
JPK
On Feb 26, 2020 8:14 PM, James Holton wrote:
In my opinion
west "true" B
factors. Atoms with high B factors don't really play a role in
determining the outer resolution limit.
-James Holton
MAD Scientist
On 3/9/2020 1:07 AM, Dale Tronrud wrote:
Just a note: James Holton said "true B-factor" not "true B-factors".
I belie
everything is converged, after we
have done all the building we can. It is this "true B factor" that is a
property of the data, not the model, and it has the relationship to
resolution and map appearance that I describe below. Does that make sense?
-James Holton
MAD Scientist
On 3/7/2020
nd Rfree higher than they are with the "natural" B
factor. You can also make your Rwork Rfree much lower by applying a
positive B factor to your data before starting refinement. This comes
with absolutely no improvement in model quality, so please don't try
this at home.
-James Holton
MAD Scien
1/2
or FSC dropping off to insignificance at 1.8 A doesn't mean you are
going to see holes in Tyr side chains. However, if you measure your
weak, high-res data really well (high multiplicity), you might be able
to sharpen your way to a much clearer map.
-James Holton
MAD Scientist
On 2/27/202
solvent mask (MSKOUT in refmac; use
phenix.fmodel with "solvent_radius" and "shrink truncation radius" taken
from phenix.refine log), and looking to see where it begins and ends.
-James Holton
MAD Scientist
On 3/4/2020 6:04 PM, Jessica Besaw wrote:
Hello friends,
I have a "blo
Which molecular dynamics package are you using?
-James Holton
MAD Scientist
On 2/28/2020 7:00 AM, Firdous Tarique wrote:
Hello everyone
I am trying to run a molecular dynamics simulation of a protein which
has a Zn atom and few phosphorylated PTMs (Thr is phosphorylated).
PTMs and Zn play
/www.grc.org/diffraction-methods-in-structural-biology-conference/2020/
So, please, let the discussion continue!
-James Holton
MAD Scientist
On 2/22/2020 11:06 AM, Nave, Colin (DLSLtd,RAL,LSCI) wrote:
Alexis
This is a very useful summary.
You say you were not convinced by Mari
re technology should be headed.
Applications are open if you'd like to join us!
https://www.grc.org/diffraction-methods-in-structural-biology-conference/2020/
-James Holton
MAD Scientist
On 2/19/2020 1:21 PM, Kay Diederichs wrote:
Dear Ana,
it is easy to ask the question (and I've been asked
ave others. Will you be one of them?
-James Holton
MAD Scientist
and Chair, 2020 GRC on Diffraction Methods in Structural Biology
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bi
Looks like the error is coming from mapmask, not sfall. Probably my
determination of the axis order got broken somehow. Can you send me log
files/example input off list?
Cheers,
-James Holton
MAD Scientist
On 1/29/2020 8:37 AM, Schulz, Eike-Christian wrote:
Dear all,
Yesterday, I have
an FOM-weighted map.
Is there a way to "change up" the statistical distribution that assigns
FOMs to hkls? Or are we stuck with this systematic error?
-James Holton
MAD Scientist
On 10/4/2019 9:31 AM, Randy Read wrote:
Hi James,
I'm sure you realise this, but it's important
imating these
maps, which gives a much more intuitive view of the "noise". You can
also look at variation of model parameters like the refined occupancy of
a ligand, which is a good way to put an "error bar" on it. The trick is
finding the right source of error to propagat
structure, the genome is incomplete.
-James Holton
MAD Scientist
On 9/16/2019 12:24 AM, John R Helliwell wrote:
Dear James,
Here you go, a “grand challenge” suggestion to consider for funding
from the “James Holton Foundation for structural biology research”:-
“The human genome/proteome in 3-D”
lbl.gov/~jamesh/challenge/diffuse/
Coming soon:
dial-a-resolution model building challenge
XFEL data processing reference set
-James Holton
MAD Scientist
On 7/25/2019 10:07 AM, Keller, Jacob wrote:
>>It would seem to me that an important issue is also: do get all
information out of
even money on equipment vs the sample.
-James Holton
MAD Scientist
On 8/30/2019 11:48 AM, Green, Todd Jason wrote:
Certainly not trying to be insulting by the suggestions but could it
be as simple an alignment issue with the crystal, issues with the beam
alignment or crystal damage
, that leaves either a genuinely ultra-sensitive protein, or some kind
of undetected equipment malfunction. Either way, we at the ALS are very
interested in this result. Would you mind trying again? And let me know
when you are coming?
-James Holton
MAD Scientist
On 8/29/2019 11:07 AM, Kimberly Stanek
What exposure time are you using? And which beamline?
-James Holton
MAD Scientist
On 8/29/2019 10:26 AM, Kimberly Stanek wrote:
Hi folks,
We have a protein that we have been trying to solve the structure of
for a while now but so far haven't been able to get any diffraction
better than
u could provide your exposure time, and perhaps
your crystal's rough size, I think you will get a lot better suggestions
about what to try next.
-James Holton
MAD Scientist
On 8/27/2019 11:14 AM, Nukri Sanishvili wrote:
Hi Lindsey,
As I mentioned to you in the separate email, 180 degrees for each
you could also be seeing
radiation-induced changes, and those are perhaps not what you are
looking for? Which data set was collected first?
-James Holton
MAD Scientist
On 1/4/2019 2:16 AM, Steiner, Roberto wrote:
Dear Piotrek
You can find some info on the use of prior phase information in
re
That's what is counter-intuitive: 2mFo-DFc amplitudes are
"designed" to be used with the slightly-wrong phase of PHIcalc, not
PHItrue.
That's what I was trying to say.
-James Holton
MAD Scientist
On 12/5/2018 7:36 PM, Keller, Jacob wrote:
That said, model phases are not so bad. In fact
the model-phased 2mFo-DFc map always has the best
correlation to the "true" map. If you substitute the "true" phases and
use the 2mFo-DFc coefficients you actually make things worse.
Counter-intuitive, but true.
-James Holton
MAD Scientist
On 12/5/2018 12:07 AM, 香
r multi-CPU programs nicely up to this
puzzling 8-10 core ceiling, but still has the GHz to run single-threaded
programs nice and fast. It's not ridiculously expensive either.
My $1,440 worth,
-James Holton
MAD Scientist
On 12/2/2018 10:56 PM, graeme.win...@diamond.ac.uk wrote:
Re: publishing be
are famous as "write-only media", but so far over
the last 10 years I haven't had any real trouble reading back an old LTO
tape.
-James Holton
MAD Scientist
On 11/29/2018 12:54 PM, Lieberman, Raquel L wrote:
Dear All,
How do your labs handle long-term raw data backups? My lab is m
fine.
My two cents,
-James Holton
MAD Scientist
On 11/26/2018 1:10 AM, V F wrote:
Dear all,
Thanks for all the off/list replies.
To be honest, how much are they paying you to take it? Can you sell it for
scrap?
May be I will give it a pass.
To compare, two dual CPU servers with Skylake Go
MTZ I have is only
from 1996.
-James Holton
MAD Scientist
On 11/9/2018 4:47 AM, Eleanor Dodson wrote:
Anyone any idea what to do about this?? Created in 1992!!
Seems unreadable..
No CTYP lines input for file: 1
Indices output even if all data items flagged "missing"
Warning,
It was brought to my attention that the link to the preprint I provided
below doesn't work, but this one does:
https://www.biorxiv.org/content/early/2018/08/18/394965
Thanks to Folmer Fredslund for pointing this out to me!
-James Holton
MAD Scientist
On 9/21/2018 3:50 PM, James Holton wrote
lots of short wedges together. May or may not
be too advanced a topic for your students? Or maybe not. As you can
guess I'm experimenting with biorxiv. So far, no comments.
Good luck with your class!
-James Holton
MAD Scientist
On 9/19/2018 5:15 PM, Whitley, Matthew J wrote:
Dear colleagues,
t
all, and in those situations you should really worry because your
competitor is also having an easy time. It is when things don't go well
that being a critically-thinking scientist is an advantage. And that, I
hope, is also good news.
Good luck!
-James Holton
MAD Scientist
On 8/14/2018 2:58
hol vapor,
especially isopropanol. You don't want to breathe that in. Best to
keep away from open flames and work in a well-ventilated area, like the
hood. Ethanol is less toxic but on a per-capita basis more dangerous.
At the very least, don't drive yourself home afterwards.
-James Holt
e middle-of-the-road
with a data retention policy like "we'll do what we can, but can't
promise anything". Even at the same synchrotron policies can vary from
beamline to beamline. So again: do you feel lucky? Do you?
-James Holton
MAD Scientist
On 7/13/2018 2:30 AM, Sergei S
lot, but other languages I'm sure will
work with a little editing.
-James Holton
MAD Scientist
On 6/28/2018 4:50 AM, Aaron Oakley wrote:
Dear CCP4ers,
The Cromer-Mann coefficients ai, bi, c (i = 1 to 4) describing the
non-dispersive part of the atomic scattering factor f(s) for a neutral atom as
a
the ACA, giving you plenty
of time to get to Boston and get on the bus.
Hope to see you there!
-James Holton
MAD Scientist
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin
idea to replace
the low-angle resolution limit with A. Just be sure your beamstop
was properly masked off.
-James Holton
MAD Scientist
On 4/5/2018 10:55 AM, Pearce, N.M. (Nick) wrote:
Could you expand a bit on what you mean by a “putative” systematic
absence? (e.g. why only the lowest order
matter what the "true" space group is, it only matters what
is in the mtz header when you run uniqueify.
Could that be what is going on?
-James Holton
MAD Scisntist
On 4/5/2018 3:52 AM, Frank von Delft wrote:
Hello - can anybody shed light on this mystery:
We need (for PanDD
After outputting the hydrogens, delete the ones you don't want and from
then on do refinement with:
make hout Y
make hydr Y
When you do that, refmac will keep the hydrogens you put in, and also
put them in the output.
-James Holton
MAD Scientist
On 3/29/2018 2:11 PM, Phil Jeffrey wrote
get better data by turning it off
once the parameters are known, that is really interesting too!
-James Holton
MAD Scientist
On 1/31/2018 1:07 AM, Kay Diederichs wrote:
Dear all,
a new BUILT of XDS is available for academic users at
http://xds.mpimf-heidelberg.mpg.de . This reverts to the ol
uld be a call to "reforigin", or origins.com, using
"ref.pdb" as the reference pdb file. Many other useful one-liners can
be found at DOI: 10.1002/spe.4380090403
Does that help?
-James Holton
MAD Scientist
On 12/18/2017 11:19 AM, Edward A. Berry wrote:
Neat idea!
And do you have
at
ambiguity, and also biases the result toward having all-positive x,y,z
values.
In case it is interesting, my script is here:
http://bl831.als.lbl.gov/~jamesh/scripts/origins.com
You need to have the CCP4 suite set up for it to work. Run it with no
arguments to get instructions.
-James Holton
e that are too fluttery
to peak above 1 sigma. The list goes on, but doing the weak-data
rejection test really helps narrow it down.
-James Holton
MAD Scientist
On 10/16/2017 3:55 AM, herman.schreu...@sanofi.com wrote:
Dear Michael,
Did you ask Phaser to check for all possible space groups? Th
I believe Gloria Borgstahl's lab at UNMC has done a little bit of work
on this.
-James Holton
MAD Scientist
On 9/16/2017 9:18 PM, Stewart, Charles E [BIOTC] wrote:
Dear all,
I am looking for suggestions on research groups that study or have
experience with aperiodic crystals
it is the difference map that tells you what to do next.
-James Holton
MAD Scientist
On 9/15/2017 4:32 AM, rohit kumar wrote:
why R/Rfree not going down from 21/25?
t is always
prudent to read the MSDS before you open a bottle, and then read the
MSDS of something similar just to put it in perspective.
-James Holton
MAD Scientist
On 9/6/2017 12:59 PM, James Holton wrote:
Was just pointed out to me off-list that my anchovy data was off, so I
just double-che
oz can, that's still ~ 1 microgram Hg as the
Anchovie Pizza Equivalent.
And it looks like one piece of bigeye tuna sushi could be as much as
~14g*1.816ppm = 25 APEs
-James Holton
MAD Scientist
On 9/6/2017 11:44 AM, James Holton wrote:
Something that could perhaps be of use here is what I like
s almost 50% bismuth by weight, a metal that is right next to mercury
on the periodic table. Brominated vegetable oil contains no bromine, by
the way. And dandruff shampoos such as Selsun Blue make an excellent
and surprisingly radiation-hard reference for the selenium edge.
-James Holton
MAD Scie
fine to convergence. What
is the peak value now?
3) set the Ba atom's f" value to twice what you expect theoretically.
Re-refine. Now what do you see?
Once you've done this, you should have a good feeling for how much of
your anomalous peak is coming from your model vs from your data.
-Ja
in the backbone
trace, or even a rotamer assignment, then doing a 0.5A jiggle isn't
going to reset that mistake. But if your trying to test the influence
of data between 1.5 A and 1.4 A, then I'd say do a jiggle of at least
half that distance.
-James Holton
MAD Scientist
On 8/17/2017
on
them. That is, re-refine the structures of interest after jiggling the
coordinates and setting all the B factors to a constant. See how
reproducible the final B factors are. This will give you an idea of how
big a change can happen by pure random chance, even with the same data.
Hope t
and setting all the B factors to a constant. See how
reproducible the final B factors are. This will give you an idea of how
big a change can happen by pure random chance, even with the same data.
Hope that helps!
-James Holton
MAD Scientist
On 8/2/2017 12:09 PM, Asmita wrote:
Hi,
This mi
Kind
of ties your hands.
I have always been a fan of erring on the side of providing information
in output files. How hard is it to delete something? How hard is it to
get it back after you deleted it?
My two cents,
-James Holton
MAD Scientist
On 7/31/2017 8:57 AM, Edwin Pozharski
once might help: http://bl831.als.lbl.gov/xtallife.html .
These days, there is no reason not to know how long your crystal will
last before you push "collect", and it is definitely worth knowing.
-James Holton
MAD Scientist
On 7/28/2017 12:21 AM, Tang Chenjun wrote:
Hi,
Thank
noise when deciding on an exposure time and spindle rotation rate. You
should either fine-slice properly, or not at all. And you should
certainly point this out when writing a grant to get an Eiger, which has
a read-out time of 3 microseconds.
-James Holton
MAD Scientist
On 7/13/2017 3:0
or
precision? Personally, I prefer to know both.
-James Holton
MAD Scientist
On 7/8/2017 11:02 AM, Frank von Delft wrote:
It is quite easy to end up with low multiplicities in the low
resolution shell, especially for low symmetry and fast-decaying crystals.
It is this scenario where Rmerge (lowres
What does Rmeas tell us that Rmerge doesn't? Given that we know the
multiplicity?
-James Holton
MAD Scientist
On 7/8/2017 9:15 AM, Frank von Delft wrote:
Anyway, back to reality: does anybody still use R statistics to
evaluate anything other than /strong/ data? Certainly I never look
gible read-out noise. But when micro crystals only give
off a handful of photons each before they die, low multiplicity might be
all you have.
-James Holton
MAD Scientist
On 7/7/2017 2:33 PM, Edward A. Berry wrote:
I think the confusion here is that the "multiplicity correction"
history to
realize that future generations seldom thank their ancestors for
"protecting" them from information.
-James Holton
MAD Scientist
On 7/5/2017 10:36 AM, Graeme Winter wrote:
Frank,
you are asking me to remove features that I like, so I would feel that the
challenge is for you to pr
ays run a Phaser job to avoid thinking about symmetry, but that is a
lot of CPU to burn up just to find a symmetry operator. Zanuda does
this internally, but doesn't seem to have a way of generating
symmetry-allowed alignments without re-refining everything. Or am I
missing something?
-James
. (2014) http://dx.doi.org/10.1107%2FS1399004714012310
Good luck!
-James Holton
MAD Scientist
On 6/21/2017 8:46 AM, Vito Calderone wrote:
I am working on a protein having 360 residues. In its sequence there are 3
Met and 5 free Cys.
I will need MAD to solve the structure since based on the sequenc
about
nearest-cell: https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi
is up, but doesn't seem to be working. Can't find 4y42 using Dong
Xiao's cell below.
Perhaps the maintainers of these pages could chime in?
-James Holton
MAD Scientist
On 6/17/2017 10:43 AM, James Holton wrote
symmetry
going on. The paper reporting 4y42 describes it as a " serendipitous
crystallization".
What happens if you try to refine your data against the model deposited
as 4y42?
Hope that helps,
-James Holton
MAD Scientist
On 6/17/2017 12:07 AM, dongxiaofei wrote:
Dear ALL,
.
All this is done automatically by the program Zanuda, but even Zanuda
cannot un-merge data. You need to provide the P1 structure factors and
then see what it tells you.
Does that help?
-James Holton
MAD Scientist
On 4/18/2017 5:56 PM, gnufreebsd wrote:
Dear Pravin
for a kinase, n lobe is quite f
/parameters is becoming too precious, then perhaps more
robust (aka time-consuming) cross-validation protocols are called for?
-James Holton
MAD Scientist
On 6/2/2015 3:26 AM, Graeme Winter wrote:
Hi Folks
Had a vague comment handed my way that xia2 assigns too many free
reflections - I have
have to carve for your density to be clear?
-James Holton
MAD Scientist
On 5/29/2015 1:15 PM, Emilia C. Arturo (Emily) wrote:
Hello.
I am struggling with an old question--old because I've found several
discussions and wiki bits on this topic, e.g. on the PyMOL mailing
list (http
nor loose information in a Fourier transform, you just
switch between representations for the same data.
HTH
-James Holton
MAD Scientist
On 5/23/2015 10:49 PM, Smith Liu wrote:
Dear All,
In the PDB file, the b-factors were only determined by the quality of
the map, is this view right
be? These are the games you play when you
don't have a beautifully clear image.
It is true, however, that if the crystal doesn't diffract at all, then
you can't use data from it to draw any conclusions.
-James Holton
MAD Scientist
On 5/24/2015 2:54 AM, Smith Liu wrote:
Dear All,
In order to acceptably
In the ADXV viewer:
http://www.scripps.edu/tainer/arvai/adxv.html
Go to Edit:Settings and click on the Small Spots radio button. This
solves most of the I can't interpret the spots problems you describe.
-James Holton
MAD Scientist
On 4/27/2015 3:31 PM, Bernhard Rupp (Hofkristallrat a.D
, negative
sigmas. Everything above that is real (Lang et al. 2014
http://dx.doi.org/10.1073/pnas.1302823110). Just difficult to build into.
-James Holton
MAD Scientist
On 4/13/2015 12:12 PM, Phoebe A. Rice wrote:
At 4A, I wouldn't unless I had an exceptionally good reason
own
kicked.mtz data files using my kick_data.com scripts, run the
refinements however you like, and then generate the RAPID map yourself
using the map_rmsd.com script that ships with the END/RAPID package.
HTH!
-James Holton
MAD Scientist
On 2/5/2015 1:03 AM, Isabel Garcia-Saez wrote:
Dear all
). In practice, if you try just
pasting in DANO from one dataset up against the F column from another
dataset then maximum likelihood phasing programs will get very cross
with you. Still trying to figure out why...
-James Holton
MAD Scientist
On 1/27/2015 12:28 AM, Frank von Delft wrote:
Hi all
for good is to write a
really amazing computer program that everyone will have to use and make
it print out the term you like?
-James Holton
MAD Scientist
On 1/17/2015 1:05 PM, rohit kumar wrote:
Dear all,
Can anyone tell me how to calculate number of frames from redundancy
or vica versa
multiplicity when you are actually averaging over errors, but
redundancy when you are not.
-James Holton
MAD Scientist
On 1/15/2015 4:14 PM, Keller, Jacob wrote:
I think a summary is that:
Background levels and errors thereof can be estimated very precisely as a
percentage of the level
that.
Nevertheless, if you count 1,000,000 photons, the sigma of that count is
1000, or 0.1% error. Something else is getting in the way. Unfortunate
really, because if we could routinely get R-meas = 0.1% we would never
need to make metal derivatives again.
-James Holton
MAD Scientist
On 1/8/2015 9
.
Finding some way to transfer information from the differences in the
working set into the free set is challenging, and indeed this is the
central problem of model building.
-James Holton
MAD Scientist
On 1/11/2015 11:05 AM, Alastair Fyfe wrote:
A related/follow-on question, hopefully on the same
the same volume evenly-cooked to
0.5 MGy is still a very good question.
Yes, it gets complicated, doesn't it? This is why I generally recommend
trying to use a beam that matches your crystal size.
-James Holton
MAD Scientist
On 12/29/2014 2:17 AM, Mohamed Noor wrote:
Dear all
In a metal
of that at the center. At twice that
distance from the center, you are down to 6.2%. The equation is
exp(-log(16)*(x/hwhm)**2) where hwhm is 1/2 of the FHWM.
HTH!
-James Holton
MAD Scientist
On 12/30/2014 12:10 PM, Keller, Jacob wrote:
Yes, it gets complicated, doesn't it? This is why I generally
rotation.
Good luck!
-James Holton
MAD Scientist
On 12/28/2014 3:12 PM, Igor Petrik wrote:
Takanori and Pierre,
Thank you for your quick responses. If you read my post you will see
that I used the xds2mos.py script to convert the xds orientation to
Mosflm format, but this gives me a result
. It ain't fast. But I'm pretty sure it works.
-James Holton
MAD Scientist
On Thu, Sep 11, 2014 at 2:44 AM, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote:
Here is a very common scenario for me.
You run several MR jobs, say to search for 2 mols/asymm unit , maybe with
different models
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 concept of
optimal filtering is all about.
HTH
-James Holton
MAD
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